From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  1 09:30:16 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01FUGLR010030;
	Tue, 1 Jan 2008 09:30:16 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01FUG0u010029;
	Tue, 1 Jan 2008 09:30:16 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01FUF8e010024;
	Tue, 1 Jan 2008 09:30:15 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01FUFpw010023;
	Tue, 1 Jan 2008 09:30:15 -0600 (CST)
Received: from ug-out-1314.google.com (ug-out-1314.google.com [66.249.92.170])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01FUBYf010016
	for <namd-l@ks.uiuc.edu>; Tue, 1 Jan 2008 09:30:12 -0600 (CST)
Received: by ug-out-1314.google.com with SMTP id a2so2741970ugf.48
        for <namd-l@ks.uiuc.edu>; Tue, 01 Jan 2008 07:30:11 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=XhcxAKjSx0NkeruOXXssqqEPHG2tViM4dMbHT7wdAgs=;
        b=VJc7rrMY88m+j2HM6fMqP9kbewe/rFGtXENhMqdaSBVdPqVfOlvaK2fevme0vQewsmLZtd7PrTX1d5nLuSUHavzdWCPvoiRA2jay3Zv2UUphp2cAkTcYjUlyJBIO01F/6HTc1iVIL0uXynSyNMICVxob2csjaMgyiZIbACed3d8=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=nONdNh5MbMAb8+v3JJ988ZS5r27okRVz0m00ziB63/wQm0lshOGwqPxZ50+fgGsHpWPI7z2nWo1/Px08l0VzQZ/zwGLunY81JVUbhBpaX0A27YwJXmUadEVnQcpi0lSszOfn6XtfiBAvOEr6x6UMxuiGjayDMLHf+oPTJP5T2XQ=
Received: by 10.67.29.20 with SMTP id g20mr12210174ugj.54.1199201410812;
        Tue, 01 Jan 2008 07:30:10 -0800 (PST)
Received: by 10.66.234.15 with HTTP; Tue, 1 Jan 2008 07:30:10 -0800 (PST)
Message-ID: <519f9e340801010730p774b02e2w76c52f85ff15344@mail.gmail.com>
Date: Tue, 1 Jan 2008 09:30:10 -0600
From: "jose correa" <corrjose@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: problems-periodic cell
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_9506_28477187.1199201410800"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_9506_28477187.1199201410800
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear all
I am running a NAMD simulacion, but the program yield this message:

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
Stack Traceback:
  [0] _ZN9HomePatch14positionsReadyEi+0x6e  [0x824ee3a]
  [1] _ZN9Sequencer17runComputeObjectsEii+0xcc  [0x82bbd5c]
  [2] _ZN9Sequencer9integrateEv+0xb04  [0x82c0894]
  [3] _ZN9Sequencer9algorithmEv+0x334  [0x82bb660]
  [4] _ZN9Sequencer9threadRunEPS_+0xc  [0x82ccd1c]
  [5] namd2 [0x831aa19]
  [6] Charm++ Runtime: Converse thread (qt_args+0x72  [0x83939ca])
~
Can somebody help me?, please.
Best wishes
Jose Correa-Basurto

------=_Part_9506_28477187.1199201410800
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<div>Dear all</div>
<div>I am running a NAMD simulacion, but the program yield this message:</div>
<div>&nbsp;</div>
<div>OPENING EXTENDED SYSTEM TRAJECTORY FILE<br>FATAL ERROR: Periodic cell has become too small for original patch grid!<br>Possible solutions are to restart from a recent checkpoint,<br>increase margin, or disable useFlexibleCell for liquid simulation.
<br>Stack Traceback:<br>&nbsp; [0] _ZN9HomePatch14positionsReadyEi+0x6e&nbsp; [0x824ee3a]<br>&nbsp; [1] _ZN9Sequencer17runComputeObjectsEii+0xcc&nbsp; [0x82bbd5c]<br>&nbsp; [2] _ZN9Sequencer9integrateEv+0xb04&nbsp; [0x82c0894]<br>&nbsp; [3] _ZN9Sequencer9algorithmEv+0x334&nbsp; [0x82bb660]
<br>&nbsp; [4] _ZN9Sequencer9threadRunEPS_+0xc&nbsp; [0x82ccd1c]<br>&nbsp; [5] namd2 [0x831aa19]<br>&nbsp; [6] Charm++ Runtime: Converse thread (qt_args+0x72&nbsp; [0x83939ca])<br>~<br>Can somebody help me?, please.</div>
<div>Best wishes</div>
<div>Jose Correa-Basurto</div>
<div><br clear="all">&nbsp;</div>

------=_Part_9506_28477187.1199201410800--


From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  1 12:21:24 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01ILO6U026714;
	Tue, 1 Jan 2008 12:21:24 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01ILOns026713;
	Tue, 1 Jan 2008 12:21:24 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01ILNmA026708;
	Tue, 1 Jan 2008 12:21:23 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01ILNF8026700;
	Tue, 1 Jan 2008 12:21:23 -0600 (CST)
Received: from an-out-0708.google.com (an-out-0708.google.com [209.85.132.242])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01ILIYm026690
	for <namd-l@ks.uiuc.edu>; Tue, 1 Jan 2008 12:21:18 -0600 (CST)
Received: by an-out-0708.google.com with SMTP id d40so916440and.114
        for <namd-l@ks.uiuc.edu>; Tue, 01 Jan 2008 10:21:18 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:cc:message-id:from:to:in-reply-to:content-type:content-transfer-encoding:mime-version:subject:date:references:x-mailer;
        bh=C0VTXl7tiePPffYvS+Ju8r3J2Dq3NKszKzT3lCQ274M=;
        b=g5hyO7Teay1pZtomN+a17aGaQJk+axaZD1V0xrDUMSLTr5G5HR9BQdbloLBnhLa4gWm1UyqvvFGTIO9s2Dxw7fc3Kn4z0fWVzeSkXDAjAC3zIgemdickEG33uXpOyUCEqNll7N3r2+mPnLFrY9QtXtoXxG4S2GWT1suk5sSIfCY=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=cc:message-id:from:to:in-reply-to:content-type:content-transfer-encoding:mime-version:subject:date:references:x-mailer;
        b=B/vnX5TU0pWSHOm4pRv2/d7J8ek1gB54Gb+OCGo0Nn1+4LZz7umQ+KS+7v4VSW/ABNz7tP0KscgU/AMU4h0px1DLJPR+5OZo1S9hdFpu9ZlBq1fMgGrta3gUqeI/cNZ3aOpCVk+gwVDIPruGzM6WAcY+jWBjSiMy5FzADskzIvc=
Received: by 10.100.239.11 with SMTP id m11mr28388375anh.70.1199211678119;
        Tue, 01 Jan 2008 10:21:18 -0800 (PST)
Received: from ?192.168.2.3? ( [76.100.169.107])
        by mx.google.com with ESMTPS id o27sm21710496ele.15.2008.01.01.10.21.14
        (version=TLSv1/SSLv3 cipher=OTHER);
        Tue, 01 Jan 2008 10:21:17 -0800 (PST)
Cc: namd-l@ks.uiuc.edu
Message-Id: <76552D83-0169-4024-9587-3A9141911726@gmail.com>
From: Christopher Gillespie <gillescche@gmail.com>
To: jose correa <corrjose@gmail.com>
In-Reply-To: <519f9e340801010730p774b02e2w76c52f85ff15344@mail.gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Content-Transfer-Encoding: 7bit
Mime-Version: 1.0 (Apple Message framework v915)
Subject: Re: namd-l: problems-periodic cell
Date: Tue, 1 Jan 2008 13:23:25 -0500
References: <519f9e340801010730p774b02e2w76c52f85ff15344@mail.gmail.com>
X-Mailer: Apple Mail (2.915)
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Jose,

You can potentially get by this by adding

margin 1.0

to you *.conf file.  I continue to increase this number until I no  
longer receive this message.

Best

Chris

On Jan 1, 2008, at 10:30 AM, jose correa wrote:

> Dear all
> I am running a NAMD simulacion, but the program yield this message:
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> FATAL ERROR: Periodic cell has become too small for original patch  
> grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
> Stack Traceback:
>   [0] _ZN9HomePatch14positionsReadyEi+0x6e  [0x824ee3a]
>   [1] _ZN9Sequencer17runComputeObjectsEii+0xcc  [0x82bbd5c]
>   [2] _ZN9Sequencer9integrateEv+0xb04  [0x82c0894]
>   [3] _ZN9Sequencer9algorithmEv+0x334  [0x82bb660]
>   [4] _ZN9Sequencer9threadRunEPS_+0xc  [0x82ccd1c]
>   [5] namd2 [0x831aa19]
>   [6] Charm++ Runtime: Converse thread (qt_args+0x72  [0x83939ca])
> ~
> Can somebody help me?, please.
> Best wishes
> Jose Correa-Basurto
>
>


From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  1 14:41:47 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01KfleA014315;
	Tue, 1 Jan 2008 14:41:47 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01KflAl014314;
	Tue, 1 Jan 2008 14:41:47 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01KflO7014310;
	Tue, 1 Jan 2008 14:41:47 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m01KflQw014309;
	Tue, 1 Jan 2008 14:41:47 -0600 (CST)
Received: from bay0-omc1-s24.bay0.hotmail.com (bay0-omc1-s24.bay0.hotmail.com [65.54.246.96])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m01Kfffs014294
	for <namd-l@ks.uiuc.edu>; Tue, 1 Jan 2008 14:41:42 -0600 (CST)
Received: from BAY122-W25 ([207.46.10.188]) by bay0-omc1-s24.bay0.hotmail.com with Microsoft SMTPSVC(6.0.3790.3959);
	 Tue, 1 Jan 2008 12:41:36 -0800
Message-ID: <BAY122-W25F88A0C32E18AFC2B9426BF510@phx.gbl>
Content-Type: multipart/alternative;
	boundary="_e229fa77-f19e-4a17-b255-6f55c9c99efc_"
X-Originating-IP: [72.234.209.206]
From: Irene Newhouse <einew@hotmail.com>
To: Christopher Gillespie <gillescche@gmail.com>,
        jose correa
	<corrjose@gmail.com>
CC: <namd-l@ks.uiuc.edu>
Subject: RE: namd-l: problems-periodic cell
Date: Tue, 1 Jan 2008 10:41:36 -1000
Importance: Normal
In-Reply-To: <76552D83-0169-4024-9587-3A9141911726@gmail.com>
References: <519f9e340801010730p774b02e2w76c52f85ff15344@mail.gmail.com>
 <76552D83-0169-4024-9587-3A9141911726@gmail.com>
MIME-Version: 1.0
X-OriginalArrivalTime: 01 Jan 2008 20:41:36.0337 (UTC) FILETIME=[B3BDAC10:01C84CB6]
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

--_e229fa77-f19e-4a17-b255-6f55c9c99efc_
Content-Type: text/plain; charset="Windows-1252"
Content-Transfer-Encoding: quoted-printable


If you are running NPT, check the most recent .xsc file for the current uni=
t cell parameters. You may have to adjust the PME grid values.
=20
Irene Newhouse> CC: namd-l@ks.uiuc.edu> From: gillescche@gmail.com> To: cor=
rjose@gmail.com> Subject: Re: namd-l: problems-periodic cell> Date: Tue, 1 =
Jan 2008 13:23:25 -0500> > Jose,> > You can potentially get by this by addi=
ng> > margin 1.0> > to you *.conf file. I continue to increase this number =
until I no > longer receive this message.> > Best> > Chris> > On Jan 1, 200=
8, at 10:30 AM, jose correa wrote:> > > Dear all> > I am running a NAMD sim=
ulacion, but the program yield this message:> >> > OPENING EXTENDED SYSTEM =
TRAJECTORY FILE> > FATAL ERROR: Periodic cell has become too small for orig=
inal patch > > grid!> > Possible solutions are to restart from a recent che=
ckpoint,> > increase margin, or disable useFlexibleCell for liquid simulati=
on.> > Stack Traceback:> > [0] _ZN9HomePatch14positionsReadyEi+0x6e [0x824e=
e3a]> > [1] _ZN9Sequencer17runComputeObjectsEii+0xcc [0x82bbd5c]> > [2] _ZN=
9Sequencer9integrateEv+0xb04 [0x82c0894]> > [3] _ZN9Sequencer9algorithmEv+0=
x334 [0x82bb660]> > [4] _ZN9Sequencer9threadRunEPS_+0xc [0x82ccd1c]> > [5] =
namd2 [0x831aa19]> > [6] Charm++ Runtime: Converse thread (qt_args+0x72 [0x=
83939ca])> > ~> > Can somebody help me?, please.> > Best wishes> > Jose Cor=
rea-Basurto> >> >>=20
_________________________________________________________________
i=92m is proud to present Cause Effect, a series about real people making a=
 difference.
http://im.live.com/Messenger/IM/MTV/?source=3Dtext_Cause_Effect=

--_e229fa77-f19e-4a17-b255-6f55c9c99efc_
Content-Type: text/html; charset="Windows-1252"
Content-Transfer-Encoding: quoted-printable

<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class=3D'hmmessage'>
If you are running NPT, check the&nbsp;most recent&nbsp;.xsc file for the c=
urrent unit cell parameters. You may have to adjust the PME grid values.<BR=
>
&nbsp;<BR>
Irene Newhouse<BR><BR>&gt; CC: namd-l@ks.uiuc.edu<BR>&gt; From: gillescche@=
gmail.com<BR>&gt; To: corrjose@gmail.com<BR>&gt; Subject: Re: namd-l: probl=
ems-periodic cell<BR>&gt; Date: Tue, 1 Jan 2008 13:23:25 -0500<BR>&gt; <BR>=
&gt; Jose,<BR>&gt; <BR>&gt; You can potentially get by this by adding<BR>&g=
t; <BR>&gt; margin 1.0<BR>&gt; <BR>&gt; to you *.conf file. I continue to i=
ncrease this number until I no <BR>&gt; longer receive this message.<BR>&gt=
; <BR>&gt; Best<BR>&gt; <BR>&gt; Chris<BR>&gt; <BR>&gt; On Jan 1, 2008, at =
10:30 AM, jose correa wrote:<BR>&gt; <BR>&gt; &gt; Dear all<BR>&gt; &gt; I =
am running a NAMD simulacion, but the program yield this message:<BR>&gt; &=
gt;<BR>&gt; &gt; OPENING EXTENDED SYSTEM TRAJECTORY FILE<BR>&gt; &gt; FATAL=
 ERROR: Periodic cell has become too small for original patch <BR>&gt; &gt;=
 grid!<BR>&gt; &gt; Possible solutions are to restart from a recent checkpo=
int,<BR>&gt; &gt; increase margin, or disable useFlexibleCell for liquid si=
mulation.<BR>&gt; &gt; Stack Traceback:<BR>&gt; &gt; [0] _ZN9HomePatch14pos=
itionsReadyEi+0x6e [0x824ee3a]<BR>&gt; &gt; [1] _ZN9Sequencer17runComputeOb=
jectsEii+0xcc [0x82bbd5c]<BR>&gt; &gt; [2] _ZN9Sequencer9integrateEv+0xb04 =
[0x82c0894]<BR>&gt; &gt; [3] _ZN9Sequencer9algorithmEv+0x334 [0x82bb660]<BR=
>&gt; &gt; [4] _ZN9Sequencer9threadRunEPS_+0xc [0x82ccd1c]<BR>&gt; &gt; [5]=
 namd2 [0x831aa19]<BR>&gt; &gt; [6] Charm++ Runtime: Converse thread (qt_ar=
gs+0x72 [0x83939ca])<BR>&gt; &gt; ~<BR>&gt; &gt; Can somebody help me?, ple=
ase.<BR>&gt; &gt; Best wishes<BR>&gt; &gt; Jose Correa-Basurto<BR>&gt; &gt;=
<BR>&gt; &gt;<BR>&gt; <BR><BR><br /><hr />i=92m is proud to present Cause E=
ffect, a series about real people making a difference. <a href=3D'http://im=
.live.com/Messenger/IM/MTV/?source=3Dtext_Cause_Effect' target=3D'_new'>Lea=
rn more</a></body>
</html>=

--_e229fa77-f19e-4a17-b255-6f55c9c99efc_--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan  2 12:35:26 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02IZQAW010588;
	Wed, 2 Jan 2008 12:35:26 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m02IZQaW010586;
	Wed, 2 Jan 2008 12:35:26 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02IZQBM010582;
	Wed, 2 Jan 2008 12:35:26 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m02IZQ50010581;
	Wed, 2 Jan 2008 12:35:26 -0600 (CST)
Received: from ro-out-1112.google.com (ro-out-1112.google.com [72.14.202.181])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02IZMIc010562
	for <namd-l@ks.uiuc.edu>; Wed, 2 Jan 2008 12:35:22 -0600 (CST)
Received: by ro-out-1112.google.com with SMTP id d36so827613roh.2
        for <namd-l@ks.uiuc.edu>; Wed, 02 Jan 2008 10:35:20 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=+zVcftlFkeVSGigP8EJAlTXqOM1KLHXxlaLW8jjKy68=;
        b=Hs5f+8akVxTC6rkuaXOgiifOyttnLYa01yjszwguMNO/3GtLxoDK0K0aj1U0TP8fxWG9/1rdqThmoQi1y3D2GQcHVMydBIOrBeaxW8+qPjtpzpfYaxuGZENdcVDvjuLsZanFO/uhTZk+TYn0NFpgzcgnJEw1Vytvg4UUrpQ2DtU=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=HVjatOv8Riw3X+jAr8n4zVlCl3jvexg7nmyZ6M46T27iLFOfgnO8Zh6T0uGnqZJEBn4gYfqRh6dzXLQBZmqm+EM9AOrzZaKaOL9qQMQh3RXvraVBPA7uB9bz6hWFRg35xfXe4kCkvz9bdEXLGukkTP8et+hLBsVTn5cyZr0gRfs=
Received: by 10.141.212.5 with SMTP id o5mr672955rvq.20.1199298919737;
        Wed, 02 Jan 2008 10:35:19 -0800 (PST)
Received: by 10.141.161.15 with HTTP; Wed, 2 Jan 2008 10:35:19 -0800 (PST)
Message-ID: <10f848910801021035j755c6da3lb42835c85d3ef9b3@mail.gmail.com>
Date: Wed, 2 Jan 2008 12:35:19 -0600
From: "snoze pa" <snoze.pa@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Help reg. input file
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_22657_14649746.1199298919718"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_22657_14649746.1199298919718
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi, I am trying to study the Zn-porphyrin system using gaussian. I did the
whole opt using gaussian. However I want to split the molecule into two
parts, Zn and P.
Does anyone have the gaussian input script for such system available. only
input file is needed in gaussian .gjf or .com format.
thanks in advance
s

------=_Part_22657_14649746.1199298919718
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi, I am trying to study the Zn-porphyrin system using gaussian. I did
the whole opt using gaussian. However I want to split the molecule into
two parts, Zn and P.<br>
Does anyone have the gaussian input script for such system available. only input file is needed in gaussian .gjf or .com format.<br>
thanks in advance<br>
s

------=_Part_22657_14649746.1199298919718--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan  2 16:20:22 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02MKMcL014064;
	Wed, 2 Jan 2008 16:20:22 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m02MKM0X014063;
	Wed, 2 Jan 2008 16:20:22 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02MKL1a014059;
	Wed, 2 Jan 2008 16:20:21 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m02MKLC2014056;
	Wed, 2 Jan 2008 16:20:21 -0600 (CST)
Received: from bristol.ks.uiuc.edu (bristol.ks.uiuc.edu [130.126.120.135])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02MKKcI014047
	(version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Wed, 2 Jan 2008 16:20:20 -0600 (CST)
Received: (from jim@localhost)
	by bristol.ks.uiuc.edu (8.13.7+Sun/8.13.8/Submit) id m02MKJB8027223
	for namd-l@ks.uiuc.edu; Wed, 2 Jan 2008 16:20:20 -0600 (CST)
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02LmTbP010309;
	Wed, 2 Jan 2008 15:48:29 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m02LmT5N010307;
	Wed, 2 Jan 2008 15:48:29 -0600 (CST)
Received: from [130.126.120.215] (abijan.ks.uiuc.edu [130.126.120.215])
	(authenticated bits=0)
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m02LmRfn010294
	(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT);
	Wed, 2 Jan 2008 15:48:27 -0600 (CST)
Message-ID: <477C06AB.10603@ks.uiuc.edu>
Date: Wed, 02 Jan 2008 15:48:27 -0600
From: Jan Saam <saam@ks.uiuc.edu>
User-Agent: Thunderbird 1.5.0.7 (X11/20060909)
MIME-Version: 1.0
To: carlos alberto gueto tettay <carlosguetot@hotmail.com>
CC: NAMD MAIL <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: charmm charge style
References: <BAY143-W1134080005D8DD937A0976D7540@phx.gbl>
In-Reply-To: <BAY143-W1134080005D8DD937A0976D7540@phx.gbl>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Dear Carlos,

curently CHARMM charges cannot yet be determined using paratool. You 
have to do it manually following the protocol described in the original 
CHARMM papers:

MacKerell Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. 
Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. 
Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. 
Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, 
R. Stote, J. Straub, M.Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. 
Karplus. 1998. All-hydrogen empirical potential for molecular modeling 
and dynamics studies of proteins using the CHARMM22 force field. J. 
Phys. Chem. B 102:3586-3616.

MacKerell Jr., A. D., J. Wiorkiewicz-Kuczera and M. Karplus 1995 An 
All-Atom Empirical Energy Function for the Simulation of Nucleic Acids 
J. Am. Chem, Soc. 117:11946-11975

Also read Alex MacKerell's Parameter development tutorial:
http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf
* 
<http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf>*other 
info can be found here:
http://mackerell.umaryland.edu/Empirical_FF_Dev.html

We are eventually going to add CHARMM charges support in Paratool, but 
it's going to take a couple more months...

Jan


carlos alberto gueto tettay wrote:
> Hi NAMD's user:
>
> I'm Carlos Gueto from UdeC, Colombia.... I'm trying to parametrize a ligand to performe my NAMD MD.... I have already made two QM calculations like the paratool user guide said..... but it doesn't say almost nothing about how determine Charmm charges... CAN SOMEBODY HELP ME ?  PLEASE... I WOULD LIKE IF YOU CAN EXPLAIN ME STEP BY STEP...
>
>
> I'll appreciate your help and time....
>
>
>
> Humbly,
>
>
>
> Carlos Alberto Gueto Tettay
> Grupo de Quimica Cuantica y Teorica
> Universidad de Cartagena
> Cartagena, Colombia
> _________________________________________________________________
> Discover the new Windows Vista
> http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBRE
>
>   


-- 

****************************************
Jan Saam
Theoretical and Computational Biophysics Group 
3061 Beckman Institute
University of Illinois
405 N. Mathews Ave
Urbana, IL 61801

Phone: (217) 244-1928
Fax:   (217) 244-6078
saam@ks.uiuc.edu


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan  3 02:05:47 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0385l80005154;
	Thu, 3 Jan 2008 02:05:47 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0385kVR005153;
	Thu, 3 Jan 2008 02:05:46 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0385kqt005149;
	Thu, 3 Jan 2008 02:05:46 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0385klA005148;
	Thu, 3 Jan 2008 02:05:46 -0600 (CST)
Received: from uwo.ca (v320-147-lb.its.uwo.ca [129.100.74.147])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0385gbo005135
	for <namd-l@ks.uiuc.edu>; Thu, 3 Jan 2008 02:05:43 -0600 (CST)
MIME-version: 1.0
Content-type: multipart/alternative;
 boundary="Boundary_(ID_pdOLZv31XBLl/HpYEVIHDA)"
Received: from zeppo.mail.uwo.pri (salk.mail.uwo.pri [172.29.32.41])
 by zeppo.mail.uwo.pri
 (Sun Java(tm) System Messaging Server 6.3-3.01 (built Jul 12 2007; 32bit))
 with ESMTP id <0JU200M656HDF6B0@zeppo.mail.uwo.pri> for namd-l@ks.uiuc.edu;
 Thu, 03 Jan 2008 03:05:37 -0500 (EST)
Received: from uwo.ca ([172.29.19.32])
 by zeppo.mail.uwo.pri (Sun Java(tm) System Messaging Server 6.3-3.01 (built
 Jul 12 2007; 32bit)) with ESMTP id <0JU200BK96HDMM10@zeppo.mail.uwo.pri> for
 namd-l@ks.uiuc.edu; Thu, 03 Jan 2008 03:05:37 -0500 (EST)
Received: from [172.29.20.33] (Forwarded-For: [172.29.20.33])
 by moranis.its.uwo.pri (mshttpd); Thu, 03 Jan 2008 03:05:37 -0500
From: "Jason Wyonn O'Young" <joyoung@uwo.ca>
To: namd-l@ks.uiuc.edu
Message-id: <f62288585d2a.477c5101@uwo.ca>
Date: Thu, 03 Jan 2008 03:05:37 -0500
X-Mailer: Sun Java(tm) System Messenger Express 6.3-3.01 (built Jul 12 2007;
 32bit)
Content-language: en
Subject: namd-l: Strange Input Error
X-Accept-Language: en
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

This is a multi-part message in MIME format.

--Boundary_(ID_pdOLZv31XBLl/HpYEVIHDA)
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT
Content-disposition: inline

Hi All,

I am having problems initiating a run on my local system.

The problem is that the .conf file works on a version compiled on another system.

When I run namd2 on my own hardware (I tried both pre-compiled and compiling myself), I get the following error:
"FATAL ERROR: Please specify either XPLOR or CHARMM format for parameters!"

I have determined that this is due to the length of a certain line in my .conf file (A tcl list for abf input). The error persists when I separate the line with backslashes or comment it out. However, when I shorten the list, it seems to work.

I am assuming it has something to do with the number of characters that is read by namd2. But, I am perplexed as to why the file works on a different system.

Thanks in advance,
Jason



--Boundary_(ID_pdOLZv31XBLl/HpYEVIHDA)
Content-type: text/html; charset=us-ascii
Content-transfer-encoding: 7BIT
Content-disposition: inline

Hi All,<br><br>I am having problems initiating a run on my local system.<br><br>The problem is that the .conf file works on a version compiled on another system.<br><br>When I run namd2 on my own hardware (I tried both pre-compiled and compiling myself), I get the following error:<br>"FATAL ERROR: Please specify either XPLOR or CHARMM format for parameters!"<br><br>I have determined that this is due to the length of a certain line in my .conf file (A tcl list for abf input). The error persists when I separate the line with backslashes or comment it out. However, when I shorten the list, it seems to work.<br><br>I am assuming it has something to do with the number of characters that is read by namd2. But, I am perplexed as to why the file works on a different system.<br><br>Thanks in advance,<br>Jason<br><br>

--Boundary_(ID_pdOLZv31XBLl/HpYEVIHDA)--


From owner-namd-l@halifax.ks.uiuc.edu Fri Jan  4 08:37:45 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m04EbjFm024300;
	Fri, 4 Jan 2008 08:37:45 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m04Ebjqe024296;
	Fri, 4 Jan 2008 08:37:45 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m04Ebjq5024289;
	Fri, 4 Jan 2008 08:37:45 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m04EbjF8024287;
	Fri, 4 Jan 2008 08:37:45 -0600 (CST)
Received: from smtp-out114.alice.it (smtp-out114.alice.it [85.37.17.114])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m04EbdUd024233
	for <namd-l@ks.uiuc.edu>; Fri, 4 Jan 2008 08:37:40 -0600 (CST)
Received: from FBCMMO02.fbc.local ([192.168.68.196]) by smtp-out114.alice.it with Microsoft SMTPSVC(6.0.3790.1830);
	 Fri, 4 Jan 2008 15:37:23 +0100
Received: from FBCMCL01B02.fbc.local ([192.168.69.83]) by FBCMMO02.fbc.local with Microsoft SMTPSVC(6.0.3790.1830);
	 Fri, 4 Jan 2008 15:37:23 +0100
Received: from megatron.local ([79.9.7.244]) by FBCMCL01B02.fbc.local with Microsoft SMTPSVC(6.0.3790.1830);
	 Fri, 4 Jan 2008 15:37:23 +0100
From: luca <bellucci14@unisi.it>
To: "'NAMD list'" <namd-l@ks.uiuc.edu>
Subject: namd-l: Coarse grained psf file and parameter
Date: Fri, 4 Jan 2008 15:37:21 +0100
User-Agent: KMail/1.9.6 (enterprise 0.20070907.709405)
MIME-Version: 1.0
Content-Type: text/plain;
  charset="us-ascii"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
Message-Id: <200801041537.21831.bellucci14@unisi.it>
X-OriginalArrivalTime: 04 Jan 2008 14:37:23.0941 (UTC) FILETIME=[51EFE950:01C84EDF]
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Dear all,
I have made my coarse grained protein model with  
 "Residue-based Coarse grained"  VMD tool.
I obtain fcoordinates and CG reverse file but I don't have psf file 
and parameter file.
where can I make/find them for protein model ?

Thanks


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  7 12:08:52 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07I8qPY020427;
	Mon, 7 Jan 2008 12:08:52 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m07I8q74020426;
	Mon, 7 Jan 2008 12:08:52 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07I8qIS020422;
	Mon, 7 Jan 2008 12:08:52 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m07I8q61020421;
	Mon, 7 Jan 2008 12:08:52 -0600 (CST)
Received: from bristol.ks.uiuc.edu (bristol.ks.uiuc.edu [130.126.120.135])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07I8lBx020412
	(version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Mon, 7 Jan 2008 12:08:47 -0600 (CST)
Received: (from jim@localhost)
	by bristol.ks.uiuc.edu (8.13.7+Sun/8.13.8/Submit) id m07I8ljo000727
	for namd-l@ks.uiuc.edu; Mon, 7 Jan 2008 12:08:47 -0600 (CST)
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m054p2BA023739;
	Fri, 4 Jan 2008 22:51:02 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m054p2Sf023738;
	Fri, 4 Jan 2008 22:51:02 -0600 (CST)
Received: from py-out-1112.google.com (py-out-1112.google.com [64.233.166.181])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m054oxMs023729
	for <namd-l@ks.uiuc.edu>; Fri, 4 Jan 2008 22:50:59 -0600 (CST)
Received: by py-out-1112.google.com with SMTP id u77so10472551pyb.15
        for <namd-l@ks.uiuc.edu>; Fri, 04 Jan 2008 20:50:58 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=y7SU1GVwqIT+/h6b8zaOpMKw0RzxQ7rjMdQWrIOjluA=;
        b=FZmwC9Oi0j2CEpstKqeonWU+1ew19JFRgunA/mv+BrHjFtFTaPyEueXHaB3IMN99JAGcZ2LUii4vGt9mhNEbPzmvggUIthMIm3Idn1/WhTEr1m3uAf3G+sRZI+hY+gQYE/ika96o2zRG2bHY08Szw97u/WAdIBBQRq4rNJ0DNuA=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=stgYKXnW2Jo34H91B9czTlyapzm2ASSugf/nmblt/xBao6uYBzYPpjKo7A+eO0IPLfufibEgyVPqONvURD1OUsufOyjGZT9HQHZNA86P049lNQI0yO29IZ/xdFRZxEKQ29PDt866JOV1rjxWf+Tu3XmuFenTR44HaKr9g2JamLI=
Received: by 10.64.53.20 with SMTP id b20mr36662909qba.40.1199508658561;
        Fri, 04 Jan 2008 20:50:58 -0800 (PST)
Received: by 10.65.84.19 with HTTP; Fri, 4 Jan 2008 20:50:58 -0800 (PST)
Message-ID: <cb60cbc40801042050r5cdf1a13g551e70894ee19142@mail.gmail.com>
Date: Sat, 5 Jan 2008 10:20:58 +0530
From: "Sangamesh B" <forum.san@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: NAMD binaries
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_1488_6550860.1199508658551"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_1488_6550860.1199508658551
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi All,

      Installed NAMD with the source package:NAMD_2.6_Source.tar.gz on AMD64
dual core, dual processor opteron system with gcc and
    MPICH2.

  The charm++ also installed and tested tests/charm++/simplearrayhello
example.

  Now the available binaries are: charmrun, flipbinpdb, flipdcd, namd2,
psfgen in ~/NAMD_2.6_Source/Linux-amd64-MPI.

  The installation ended with no errors, but with a message something like:

  echo "#!/bin/sh\necho unavailable on this platform"


  Can any one tell me whether installation is successful?

  regards,
  Sangamesh
  HPC Engineer

------=_Part_1488_6550860.1199508658551
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<span style="color: rgb(51, 51, 255);">Hi All,</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Installed NAMD with the source package:NAMD_2.6_Source.tar.gz on AMD64 dual core, dual processor opteron system with gcc and
</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; &nbsp; MPICH2.</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; The charm++ also installed and tested tests/charm++/simplearrayhello example.
</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; Now the available binaries are: charmrun, flipbinpdb, flipdcd, namd2, psfgen in ~/NAMD_2.6_Source/Linux-amd64-MPI.
</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; The installation ended with no errors, but with a message something like:</span><br style="color: rgb(51, 51, 255);">
<br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; echo &quot;#!/bin/sh\necho unavailable on this platform&quot;</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">
&nbsp; </span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; Can any one tell me whether installation is successful?</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">&nbsp; regards,</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">&nbsp; Sangamesh</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">
&nbsp; HPC Engineer</span><br>

------=_Part_1488_6550860.1199508658551--


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  7 13:41:52 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07JfqBi008153;
	Mon, 7 Jan 2008 13:41:52 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m07JfqH9008152;
	Mon, 7 Jan 2008 13:41:52 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07Jfp7P008148;
	Mon, 7 Jan 2008 13:41:51 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m07Jfpfe008147;
	Mon, 7 Jan 2008 13:41:51 -0600 (CST)
Received: from py-out-1112.google.com (py-out-1112.google.com [64.233.166.179])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m07JfmXI008139
	for <namd-l@ks.uiuc.edu>; Mon, 7 Jan 2008 13:41:48 -0600 (CST)
Received: by py-out-1112.google.com with SMTP id u77so11511840pyb.15
        for <namd-l@ks.uiuc.edu>; Mon, 07 Jan 2008 11:41:48 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=KPILMTtFcvpMSBXqgQ74qcQHzuEcO13v6gnJLLCR0L0=;
        b=NVamDHDCfC78JOiQ2WmcfTAaqgUsZAUIiCMYl0RXMAq0N78jLgojF4l49CQs9uYGYSUqBv5sDC9Pq03kYXE8tiKYDaRYNVeHiYKph3xAWdktrE6IsfERZmvZ5Dfn3gl2TpM75LdVzqK9kBYvauu93WHG8QPG8qLDawUHcwfFMlE=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=IQb3xnFznGD1Rg2pHOFT2byN9uQYJhv+txUjOf09Kk0t1tM3hS8OS2H+MFwqhQzINdZDljwHt99bYNzO/OyRjrmpEXiVVTlafDt7WWx584qHxqXNPQMkePyLZubvo6I72bjZx66/hlYmKd/P3T+taOR6oMfJsIZvbX2OdNyJzO4=
Received: by 10.141.171.6 with SMTP id y6mr10836781rvo.143.1199734907543;
        Mon, 07 Jan 2008 11:41:47 -0800 (PST)
Received: by 10.141.194.13 with HTTP; Mon, 7 Jan 2008 11:41:47 -0800 (PST)
Message-ID: <10f848910801071141o7cb7dea4p85f78f012a6261eb@mail.gmail.com>
Date: Mon, 7 Jan 2008 13:41:47 -0600
From: "snoze pa" <snoze.pa@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Help
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_13753_23348260.1199734907557"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_13753_23348260.1199734907557
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear NAMD users,

 I am trying to simulate HEME using NAMD. I am using the right patch but
after minimization the central Fe is moving a little away from the hem
plane, at least 0.5A. Any idea, or help so that I can fix the Fe in the
center of the P ring.
Thanks in advance.
s

------=_Part_13753_23348260.1199734907557
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear NAMD users,<br><br>&nbsp;I am trying to simulate HEME using NAMD. I am using the right patch but after minimization the central Fe is moving a little away from the hem plane, at least 0.5A. Any idea, or help so that I can fix the Fe in the center of the P ring.
<br>Thanks in advance.<br>s<br>

------=_Part_13753_23348260.1199734907557--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan  9 10:04:34 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09G4YEV026213;
	Wed, 9 Jan 2008 10:04:34 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m09G4XrH026212;
	Wed, 9 Jan 2008 10:04:33 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09G4XNx026207;
	Wed, 9 Jan 2008 10:04:33 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m09G4XDx026206;
	Wed, 9 Jan 2008 10:04:33 -0600 (CST)
Received: from emroute2.ornl.gov (emroute2.ornl.gov [160.91.86.17])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09G4SOf026166
	for <namd-l@ks.uiuc.edu>; Wed, 9 Jan 2008 10:04:28 -0600 (CST)
Received: from emroute2.ornl.gov ([127.0.0.1])
 by emroute2.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUD00LJ0WN85O@emroute2.ornl.gov> for namd-l@ks.uiuc.edu; Wed,
 09 Jan 2008 11:04:20 -0500 (EST)
Received: from CONVERSION-DAEMON.emroute2.ornl.gov by emroute2.ornl.gov
 (PMDF V6.3-x14 #31501) id <0JUD00301WN804@emroute2.ornl.gov> for
 namd-l@ks.uiuc.edu; Wed, 09 Jan 2008 11:04:20 -0500 (EST)
Received: from ORNLEXCHANGE.ornl.gov (ornlexchange1.ornl.gov [160.91.1.20])
 by emroute2.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUD000FKWN79D@emroute2.ornl.gov> for namd-l@ks.uiuc.edu; Wed,
 09 Jan 2008 11:04:20 -0500 (EST)
Date: Wed, 09 Jan 2008 11:04:19 -0500
From: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: namd-l: ABF question
To: namd-l@ks.uiuc.edu
Message-id: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
MIME-version: 1.0
X-MIMEOLE: Produced By Microsoft Exchange V6.5
Content-type: text/plain; charset=iso-8859-1
Thread-Topic: ABF question
Thread-Index: AchS2UrbxRRTtXA4RY683IzgM7V8BQ==
Content-class: urn:content-classes:message
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id m09G4SOf026186
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk


Hi All,

I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small? 

I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful. 

Jiancong


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan  9 11:27:02 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09HR2Zp008138;
	Wed, 9 Jan 2008 11:27:02 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m09HR2J9008137;
	Wed, 9 Jan 2008 11:27:02 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09HR1YR008132;
	Wed, 9 Jan 2008 11:27:01 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m09HR1Al008131;
	Wed, 9 Jan 2008 11:27:01 -0600 (CST)
Received: from wx-out-0506.google.com (wx-out-0506.google.com [66.249.82.226])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m09HQw47008122
	for <namd-l@ks.uiuc.edu>; Wed, 9 Jan 2008 11:26:58 -0600 (CST)
Received: by wx-out-0506.google.com with SMTP id h27so163433wxd.3
        for <namd-l@ks.uiuc.edu>; Wed, 09 Jan 2008 09:26:57 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        bh=Gbtk+YOsgzzC2t1+LbXCIsWDLOmWrZ8uYJXkbERuY7g=;
        b=cSQMzd2Gzf0aRHI+EtrQOhhsj1g0z5ZOsdJcLWt9kJpINH+fiY94miJ/aeOIkGTQmkgCsp3X6JSvcqYkgwPisGRIRivWpcJkwpNJ4W3LaiX8BU+kohwqsYool3xO3TWoYKW448D7uAhSK5KkIEbIajH2hwYw4XGInK+BJ6CePpI=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        b=j7Yjk8fv7P5/ySwMAMhmFF3hf0tFW71WvFRAEh4asSdpXnuC0EXwV0rwgf9H7H/lG9g9yR4AlSOX6NuwXGpO5Ap1b1m3ql1ZCu2gtT0PtGcEnaaj25As04PeRoiWV58ohKkAqczTV1Sxq8QqacAMVEcv0h6HaYO+mVL12m3Q+/M=
Received: by 10.150.229.16 with SMTP id b16mr360141ybh.115.1199899617532;
        Wed, 09 Jan 2008 09:26:57 -0800 (PST)
Received: by 10.35.58.18 with HTTP; Wed, 9 Jan 2008 09:26:57 -0800 (PST)
Message-ID: <a61b1c250801090926y1f11b1ccrb51831d97f49038f@mail.gmail.com>
Date: Wed, 9 Jan 2008 12:26:57 -0500
From: "Jerome Henin" <jhenin@cmm.chem.upenn.edu>
To: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: Re: namd-l: ABF question
Cc: namd-l@ks.uiuc.edu
In-Reply-To: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
References: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
X-Google-Sender-Auth: 75073fb4228163ee
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Hi Jiancong,

It is best to prepare an equilibrated system with the RC in the
desired range, using any kind of appropriate restraints. The boundary
biases of ABF are harmonic - if you start far away from the min or max
value, the excessive pulling on the system may have side-effects.

An ABF tutorial is in preparation. We will announce it on this mailing
list when it goes online - this should not take very long.

Jerome

On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
>
> Hi All,
>
> I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?
>
> I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.
>
> Jiancong
>
>


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 10 09:33:55 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0AFXsgS009014;
	Thu, 10 Jan 2008 09:33:54 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0AFXs0m009013;
	Thu, 10 Jan 2008 09:33:54 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0AFXsCm009008;
	Thu, 10 Jan 2008 09:33:54 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0AFXsI9009007;
	Thu, 10 Jan 2008 09:33:54 -0600 (CST)
Received: from py-out-1112.google.com (py-out-1112.google.com [64.233.166.183])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0AFXnOo008998
	for <namd-l@ks.uiuc.edu>; Thu, 10 Jan 2008 09:33:49 -0600 (CST)
Received: by py-out-1112.google.com with SMTP id u77so938031pyb.15
        for <namd-l@ks.uiuc.edu>; Thu, 10 Jan 2008 07:33:49 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=s6C7SwqjmrAC0PGB5Lq8giUxcO1BHW2pGInaJJtBIEA=;
        b=WNNmk8ujF6vW24kUgychIq07p2sWv3zhjoXMJKCQFc8iKYXEmJ9GF+e8pxZWmHWGFiajDXMNi7ECe8iRJX+0JCiYe7j/tMz0Fw2++ZG7ZRvihJ6+isDBrNbQJX2xVifrAxfO5TmWCS9zDnPKO/dNPTkpgvql57ITUsEf0+ZpZjE=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=Hy3kSuaUsXuSSIrVFGrIC8Z/L7wjISHTgNTV0/3LB+Le0KgMcLd1k64NUkNhgAMKJVUEW1fhclnW494hubMjZlFU1jwr2+InM/yt/xNrasiq/mUmduKRpqvDM3ePg0CLgdw68se8itIfyyMQYHR8dtwdGqnv9V7IhNDVzyljGYU=
Received: by 10.65.15.19 with SMTP id s19mr4560863qbi.17.1199979229237;
        Thu, 10 Jan 2008 07:33:49 -0800 (PST)
Received: by 10.64.232.20 with HTTP; Thu, 10 Jan 2008 07:33:49 -0800 (PST)
Message-ID: <5b4c48b30801100733y20211f3aneb81fa7e02f1f45a@mail.gmail.com>
Date: Thu, 10 Jan 2008 09:33:49 -0600
From: "Alex Huang" <xjtuhw@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Question about Error Message
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_7768_19025975.1199979229191"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_7768_19025975.1199979229191
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi there,

When I use NAMD, I came across this error msg: DIDN'T FIND "NATOM" IN PSF
FILE ../ionized.psf

However, I look it up in my psf file. There does have "55258 !NATOM" in my
psf file.

How come this error message? And what should I do to solve it?

Thanks a lot!

Best wishes,
Alex

------=_Part_7768_19025975.1199979229191
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi there,<br><br>When I use NAMD, I came across this error msg: DIDN&#39;T FIND &quot;NATOM&quot; IN PSF FILE ../ionized.psf<br><br>However, I look it up in my psf file. There does have &quot;55258 !NATOM&quot; in my psf file.
<br><br>How come this error message? And what should I do to solve it?<br><br>Thanks a lot!<br><br>Best wishes,<br>Alex<br>

------=_Part_7768_19025975.1199979229191--


From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 11 16:06:32 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BM6WEK026287;
	Fri, 11 Jan 2008 16:06:32 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0BM6WuE026286;
	Fri, 11 Jan 2008 16:06:32 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BM6VJ3026279;
	Fri, 11 Jan 2008 16:06:32 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0BM6Vg4026277;
	Fri, 11 Jan 2008 16:06:31 -0600 (CST)
Received: from bristol.ks.uiuc.edu (bristol.ks.uiuc.edu [130.126.120.135])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BM6RRt026270
	(version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Fri, 11 Jan 2008 16:06:27 -0600 (CST)
Received: (from jim@localhost)
	by bristol.ks.uiuc.edu (8.13.7+Sun/8.13.8/Submit) id m0BM6RWD005499
	for namd-l@ks.uiuc.edu; Fri, 11 Jan 2008 16:06:27 -0600 (CST)
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BFLt3l027451;
	Fri, 11 Jan 2008 09:21:55 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0BFLtS5027450;
	Fri, 11 Jan 2008 09:21:55 -0600 (CST)
Received: from relay8.mail.ox.ac.uk (relay8.mail.ox.ac.uk [129.67.1.171])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BFLots027441
	for <namd-l@ks.uiuc.edu>; Fri, 11 Jan 2008 09:21:50 -0600 (CST)
Received: from smtp2.mail.ox.ac.uk ([163.1.2.205])
	by relay8.mail.ox.ac.uk with esmtp (Exim 4.68)
	(envelope-from <philip.fowler@bioch.ox.ac.uk>)
	id 1JDLhd-0005XY-Qt
	for namd-l@ks.uiuc.edu; Fri, 11 Jan 2008 15:21:49 +0000
Received: from nak.bioch.ox.ac.uk ([129.67.76.21])
	by smtp2.mail.ox.ac.uk with esmtpsa (TLSv1:AES128-SHA:128)
	(Exim 4.68)
	(envelope-from <philip.fowler@bioch.ox.ac.uk>)
	id 1JDLhd-0004Dv-7A
	for namd-l@ks.uiuc.edu; Fri, 11 Jan 2008 15:21:49 +0000
Message-Id: <262E40DD-5A67-4496-AE86-51D5538B8E5E@bioch.ox.ac.uk>
From: Philip Fowler <philip.fowler@bioch.ox.ac.uk>
To: namd-l@ks.uiuc.edu
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Content-Transfer-Encoding: 7bit
Mime-Version: 1.0 (Apple Message framework v915)
Subject: namd-l: ABF using distance-com but with negative xiMin
Date: Fri, 11 Jan 2008 15:21:48 +0000
X-Mailer: Apple Mail (2.915)
X-Oxford-Username: bioc0692
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Hi,

I am using the adaptive biased forcing method to calculate the  
potential of mean force through a pore. I therefore define abf1 as the  
atoms lining the pore and abf2 as the ion I am moving through the pore.

My problem is that xiMin seems only to be able to take positive values  
even if I set it to be negative which I need in order to move the ion  
all the way along the pore.

(a) Am I correct that xiMin can only be >= 0 for distance-com?
(b) If so, does anyone have another ABF reaction coordinate Tcl file  
that fixes this
(c) or does anyone have any other ideas?

Thanks,

--Phil Fowler


From owner-namd-l@halifax.ks.uiuc.edu Fri Jan 11 17:19:40 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BNJdnD004781;
	Fri, 11 Jan 2008 17:19:39 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0BNJdvT004780;
	Fri, 11 Jan 2008 17:19:39 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BNJdep004774;
	Fri, 11 Jan 2008 17:19:39 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0BNJdGi004773;
	Fri, 11 Jan 2008 17:19:39 -0600 (CST)
Received: from hs-out-2122.google.com (hs-out-0708.google.com [64.233.178.244])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0BNJWqJ004755
	for <namd-l@ks.uiuc.edu>; Fri, 11 Jan 2008 17:19:32 -0600 (CST)
Received: by hs-out-2122.google.com with SMTP id l65so1265372hsc.0
        for <namd-l@ks.uiuc.edu>; Fri, 11 Jan 2008 15:19:32 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        bh=qMfRbxjBCIvS4DlMIPro94j2Hl3uhviwGDv4pBrqDhw=;
        b=wiqQnlynAEjkdwmEqUxAKjcU7g+OmCInhQ5qKrj1ivG7/wfbAtMIl2TD//Jtqti/L1Pl3ZCXGcBLTo2hn+bfZVe4R8eJSrXQO4z6XHvRqzSDF98gOSNjMTNsuD/ELUtSrogZ1YtRjq8w1n/FwDuj2990Ie0ZcLNEqAWP3/ndGkc=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        b=aqHw8FeefBAq9KGtAFf3Fj9nOlRNUjXMmXoDlcCNy0nMF0G8b4qpwZMGDRHS8wAIOM25aRD6BN699GOftS46oMJ4IiZnjRJaRQvZkb015XOKaj2k+UWP5s6ekZJopIV59Z9E+QDMSx2o5ZadIj3Y9qwxj1lUvqXKefb3wP0op58=
Received: by 10.150.153.19 with SMTP id a19mr1570634ybe.107.1200093572253;
        Fri, 11 Jan 2008 15:19:32 -0800 (PST)
Received: by 10.150.123.20 with HTTP; Fri, 11 Jan 2008 15:19:32 -0800 (PST)
Message-ID: <a61b1c250801111519o6d77038dy7c60fe0fe4f10ad6@mail.gmail.com>
Date: Fri, 11 Jan 2008 18:19:32 -0500
From: "Jerome Henin" <jhenin@cmm.chem.upenn.edu>
To: "Philip Fowler" <philip.fowler@bioch.ox.ac.uk>
Subject: Re: namd-l: ABF using distance-com but with negative xiMin
Cc: namd-l@ks.uiuc.edu
In-Reply-To: <262E40DD-5A67-4496-AE86-51D5538B8E5E@bioch.ox.ac.uk>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
References: <262E40DD-5A67-4496-AE86-51D5538B8E5E@bioch.ox.ac.uk>
X-Google-Sender-Auth: b326884e838574ac
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Hi Phil, good to hear from you!

Yes, distance-com is a "real" distance, hence always positive. For
your purpose, I'd suggest zCoord if your pore is aligned along the z
direction. zCoord is an algebraic distance (really the dot product of
a vector and a reference axis).

Let me know how that works for you.
Jerome

On Jan 11, 2008 10:21 AM, Philip Fowler <philip.fowler@bioch.ox.ac.uk> wrote:
> Hi,
>
> I am using the adaptive biased forcing method to calculate the
> potential of mean force through a pore. I therefore define abf1 as the
> atoms lining the pore and abf2 as the ion I am moving through the pore.
>
> My problem is that xiMin seems only to be able to take positive values
> even if I set it to be negative which I need in order to move the ion
> all the way along the pore.
>
> (a) Am I correct that xiMin can only be >= 0 for distance-com?
> (b) If so, does anyone have another ABF reaction coordinate Tcl file
> that fixes this
> (c) or does anyone have any other ideas?
>
> Thanks,
>
> --Phil Fowler
>
>


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 07:12:13 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EDCDeF011311;
	Mon, 14 Jan 2008 07:12:13 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EDCDpm011310;
	Mon, 14 Jan 2008 07:12:13 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EDCCwv011306;
	Mon, 14 Jan 2008 07:12:12 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EDCCbU011305;
	Mon, 14 Jan 2008 07:12:12 -0600 (CST)
Received: from s12.pixelx.de (s12.pixelx.de [80.86.184.34])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EDC7Nb011284
	(version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 07:12:08 -0600 (CST)
X-Envelope-To: <namd-l@ks.uiuc.edu>
Received: from s12.pixelx.de (localhost [127.0.0.1])
	by s12.pixelx.de (8.13.1/8.11.6) with ESMTP id m0EDBqUq027921
	(using TLSv1/SSLv3 with cipher EDH-RSA-DES-CBC3-SHA (168 bits) verified NO)
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 14:11:52 +0100
Received: (from wwwrun@localhost)
	by s12.pixelx.de (8.13.1/8.12.3/Debian-5) id m0EDBqDd027920;
	Mon, 14 Jan 2008 14:11:52 +0100
Date: Mon, 14 Jan 2008 14:11:52 +0100
Message-Id: <200801141311.m0EDBqDd027920@s12.pixelx.de>
X-Authentication-Warning: s12.pixelx.de: wwwrun set sender to michael@perfect-kreim.de using -f
To: namd-l@ks.uiuc.edu
Subject: namd-l: =?ISO-8859-1?Q?changing position of ?=  =?ISO-8859-1?Q?atoms during NAMD sim?=  =?ISO-8859-1?Q?ulation?=
From: michael@perfect-kreim.de
X-Priority: 3
Importance: Normal
X-MSMail-Priority: Normal
X-MimeOLE: Produced by Confixx WebMail
X-Mailer: Confixx WebMail (like SquirrelMail)
Cc: 
MIME-Version: 1.0
Content-Type: text/plain; charset="ISO-8859-1"
Content-Transfer-Encoding: 7bit
X-Greylist: Sender is SPF-compliant, not delayed by milter-greylist-3.0 (s12.pixelx.de [0.0.0.0]); Mon, 14 Jan 2008 14:11:52 +0100 (CET)
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Hi all,

for my diploma-thesis I need a system to change the position of atoms
during simulation.
What I am planing to do is:
I have a water-box with ions and every time an ion crosses a given
z-coordinate the ion should be moved back to its "site" of the box.
I cannot work with forces or constrains, because I need the number of
atoms that cross the z-coordinate and I need fixed concentrations.
So I have to reset the coordinate of the ion.

My main question is:
Is it possible with NAMD (and VMD or another program) to change the
coordinates of atoms during simulation if the coordinates exceed a given
value?

I tried to enter some TCL-code in my NAMD-config-file, but this code is
only executed once and not every timestep.

Then I found this "Interactive Molecular Dynamics Simulation"-thing but
as far as I understand it, it can only apply forces.

Maybe there is a possibility to write some plugin for NAMD?
I am open to anything.

Thanks a lot for your answer.

Best regards,

Michael




From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 11:11:34 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHBYdW018180;
	Mon, 14 Jan 2008 11:11:34 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHBYon018179;
	Mon, 14 Jan 2008 11:11:34 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHBYOm018174;
	Mon, 14 Jan 2008 11:11:34 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHBY08018172;
	Mon, 14 Jan 2008 11:11:34 -0600 (CST)
Received: from bristol.ks.uiuc.edu (bristol.ks.uiuc.edu [130.126.120.135])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHBTaX018159
	(version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 11:11:29 -0600 (CST)
Received: (from jim@localhost)
	by bristol.ks.uiuc.edu (8.13.7+Sun/8.13.8/Submit) id m0EHBT9S007218
	for namd-l@ks.uiuc.edu; Mon, 14 Jan 2008 11:11:29 -0600 (CST)
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0DItpdU016185;
	Sun, 13 Jan 2008 12:55:51 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0DItpdE016184;
	Sun, 13 Jan 2008 12:55:51 -0600 (CST)
Received: from emroute1.ornl.gov (emroute1.ornl.gov [160.91.4.119])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0DItkEn016120
	for <namd-l@ks.uiuc.edu>; Sun, 13 Jan 2008 12:55:46 -0600 (CST)
Received: from emroute1.ornl.gov ([127.0.0.1])
 by emroute1.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUL00J7CJ8PAC@emroute1.ornl.gov> for namd-l@ks.uiuc.edu; Sun,
 13 Jan 2008 13:55:38 -0500 (EST)
Received: from CONVERSION-DAEMON.emroute1.ornl.gov by emroute1.ornl.gov
 (PMDF V6.3-x14 #31501) id <0JUL00301J8PZ5@emroute1.ornl.gov>; Sun,
 13 Jan 2008 13:55:37 -0500 (EST)
Received: from ORNLEXCHANGE.ornl.gov (ornlexchange1.ornl.gov [160.91.1.20])
 by emroute1.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUL002VAJ8P9K@emroute1.ornl.gov>; Sun,
 13 Jan 2008 13:55:37 -0500 (EST)
Received: from ornl15 ([160.91.2.150]) by ORNLEXCHANGE.ornl.gov with Microsoft
 SMTPSVC(6.0.3790.3959); Sun, 13 Jan 2008 13:55:37 -0500
Date: Sun, 13 Jan 2008 13:55:37 -0500
From: jia <jia@ornl.gov>
Subject: RE: namd-l: ABF question
To: Jerome Henin <jhenin@cmm.chem.upenn.edu>
Cc: namd-l <namd-l@ks.uiuc.edu>
Message-id: <47871543@ornl15>
MIME-version: 1.0
X-Mailer: Infinite Mobile Delivery (Hydra) SMTP v3.62.01
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit
X-WebMail-UserID: jia@ornl.gov
X-EXP32-SerialNo: 00002415
X-OriginalArrivalTime: 13 Jan 2008 18:55:37.0954 (UTC)
 FILETIME=[E2CE6C20:01C85615]
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Hi Jerome and NAMD users,

I started over with better configurations and it seems working now. However, 
the new problem is that the RC is not equally sampled. I've tried with 
different interval, initial configurations and bin width, and one of the 
borders is always oversampled than the rest. I would greatly appreciate any 
help and advice. Thanks much.

Jiancong

>===== Original Message From Jerome Henin <jhenin@cmm.chem.upenn.edu> =====
>Hi Jiancong,
>
>It is best to prepare an equilibrated system with the RC in the
>desired range, using any kind of appropriate restraints. The boundary
>biases of ABF are harmonic - if you start far away from the min or max
>value, the excessive pulling on the system may have side-effects.
>
>An ABF tutorial is in preparation. We will announce it on this mailing
>list when it goes online - this should not take very long.
>
>Jerome
>
>On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
>>
>> Hi All,
>>
>> I'm performing an ABF calculations with the reaction coordinate spanning 
between 20 and 30 A defined by "distance-com". The reaction coordinate was 
split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 
100ps long, no single data point fell into the 25-30 A range. Does this mean 
the default force constant applied at the borders of the reaction coordinate 
(10 kcal/mol/A2) is too small?
>>
>> I'm also wondering if there's any ABF tutorial available on NAMD website 
with all the input files for a model system. That'd be greatly helpful.
>>
>> Jiancong
>>
>>

Postdoc Research fellow
Center for Molecular Biophysics,
Oak Ridge National Lab
Oak Ridge, TN, 37830


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 11:02:42 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EH2gxp017010;
	Mon, 14 Jan 2008 11:02:42 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EH2fsj017009;
	Mon, 14 Jan 2008 11:02:41 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EH2fvY017005;
	Mon, 14 Jan 2008 11:02:41 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EH2fQf017004;
	Mon, 14 Jan 2008 11:02:41 -0600 (CST)
Received: from wr-out-0506.google.com (wr-out-0506.google.com [64.233.184.226])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EH2a7R016995
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 11:02:36 -0600 (CST)
Received: by wr-out-0506.google.com with SMTP id c49so600222wra.21
        for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 09:02:36 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        bh=8+t9V8WMpd7mvCvP4bkV7tQqGhNhocnXoKqIFZcE/Mc=;
        b=kA/Dyb2A+du+2FOgc353QPViSMRISogJXWPH0rUWAyyQ6NrOOXFCAFdMt3S9+E5i26EtoTWPo5AgvhSJEXe2FHWIasFfXsOCr0px+3MWGdDSLSFsLrFHnbv5eF0CKEsP3Y71NxhT3F0GWmi5f4kn5gGCJchasurgdwPONDHTKeI=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        b=uorYhdUyjd7Af//cyrlc2RfmpbZE+HgeJo47z9cynPrlJjkK+VK/TZcKe7nK/7IW5VedcBtGWojw16EF26g2KrpCdZ51TOVbVb3NPhg/PnZBGYLJ5+S4CS8o7CrRX2n+V7petwVUQpxyL5Z9HQDRbzVe/8o/WLizlS3Dp0yPZ8w=
Received: by 10.150.205.13 with SMTP id c13mr2508323ybg.135.1200330155947;
        Mon, 14 Jan 2008 09:02:35 -0800 (PST)
Received: by 10.150.123.20 with HTTP; Mon, 14 Jan 2008 09:02:35 -0800 (PST)
Message-ID: <a61b1c250801140902x773efe2l4451cd05b2f117ae@mail.gmail.com>
Date: Mon, 14 Jan 2008 12:02:35 -0500
From: "Jerome Henin" <jhenin@cmm.chem.upenn.edu>
To: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: Re: namd-l: ABF question
Cc: namd-l@ks.uiuc.edu
In-Reply-To: <E970EE66714B5741A9CF3C407B8605780504D3D2@ORNLEXCHANGE.ornl.gov>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
References: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
	 <a61b1c250801090926y1f11b1ccrb51831d97f49038f@mail.gmail.com>
	 <E970EE66714B5741A9CF3C407B8605780504D3D2@ORNLEXCHANGE.ornl.gov>
X-Google-Sender-Auth: e7517a5abbe37eda
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Jiancong,
I'm afraid I cannot tell you much that has not been discussed on this
list before with other users, mostly to check for non-equilibrium
pulling effects and the influence of the fullSamples parameter. It
might be that your new starting configurations are not yet
well-equilibrated. It might be that there are other very slow degrees
of freedom in the system, interfering with your calculation.
Jerome

On Jan 14, 2008 11:14 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
>
> Hi Jerome and NAMD users,
>
> I started over with better configurations and it seems working now. However, the new problem is that the RC is not equally sampled. I've tried with different interval, initial configurations and bin width, and one of the borders is always oversampled than the rest. I would greatly appreciate any help and advice. Thanks much.
>
> Jiancong
>
>
>
>
>
> -----Original Message-----
> From: heninj@gmail.com on behalf of Jerome Henin
> Sent: Wed 1/9/2008 12:26 PM
> To: Xu, Jiancong
> Cc: namd-l@ks.uiuc.edu
> Subject: Re: namd-l: ABF question
>
>
> Hi Jiancong,
>
> It is best to prepare an equilibrated system with the RC in the
> desired range, using any kind of appropriate restraints. The boundary
> biases of ABF are harmonic - if you start far away from the min or max
> value, the excessive pulling on the system may have side-effects.
>
> An ABF tutorial is in preparation. We will announce it on this mailing
> list when it goes online - this should not take very long.
>
> Jerome
>
> On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
> >
> > Hi All,
> >
> > I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?
> >
> > I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.
> >
> > Jiancong
> >
> >
>
>


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 10:14:40 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EGEeAl010093;
	Mon, 14 Jan 2008 10:14:40 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EGEej9010090;
	Mon, 14 Jan 2008 10:14:40 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EGEdFa010086;
	Mon, 14 Jan 2008 10:14:39 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EGEdls010085;
	Mon, 14 Jan 2008 10:14:39 -0600 (CST)
Received: from emroute1.ornl.gov (emroute1.ornl.gov [160.91.4.119])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EGEYBC010069
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 10:14:34 -0600 (CST)
Received: from emroute1.ornl.gov ([127.0.0.1])
 by emroute1.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUN007BT6GAMR@emroute1.ornl.gov> for namd-l@ks.uiuc.edu; Mon,
 14 Jan 2008 11:14:34 -0500 (EST)
Received: from CONVERSION-DAEMON.emroute1.ornl.gov by emroute1.ornl.gov
 (PMDF V6.3-x14 #31501) id <0JUN00D016G9D1@emroute1.ornl.gov>; Mon,
 14 Jan 2008 11:14:34 -0500 (EST)
Received: from ORNLEXCHANGE.ornl.gov (ornlexchange1.ornl.gov [160.91.1.20])
 by emroute1.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUN00FX46G9E1@emroute1.ornl.gov>; Mon,
 14 Jan 2008 11:14:33 -0500 (EST)
Date: Mon, 14 Jan 2008 11:14:07 -0500
From: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: RE: namd-l: ABF question
To: Jerome Henin <jhenin@cmm.chem.upenn.edu>
Cc: namd-l@ks.uiuc.edu
Message-id: <E970EE66714B5741A9CF3C407B8605780504D3D2@ORNLEXCHANGE.ornl.gov>
MIME-version: 1.0
X-MIMEOLE: Produced By Microsoft Exchange V6.5
Content-type: text/plain; charset=iso-8859-1
Thread-Topic: namd-l: ABF question
Thread-Index: AchS5Nv4+nUSku8TS/O4NEs2ILHcnAD46FgX
Content-class: urn:content-classes:message
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
References: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
 <a61b1c250801090926y1f11b1ccrb51831d97f49038f@mail.gmail.com>
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id m0EGEYBC010074
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk


Hi Jerome and NAMD users,

I started over with better configurations and it seems working now. However, the new problem is that the RC is not equally sampled. I've tried with different interval, initial configurations and bin width, and one of the borders is always oversampled than the rest. I would greatly appreciate any help and advice. Thanks much.

Jiancong





-----Original Message-----
From: heninj@gmail.com on behalf of Jerome Henin
Sent: Wed 1/9/2008 12:26 PM
To: Xu, Jiancong
Cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: ABF question
 
Hi Jiancong,

It is best to prepare an equilibrated system with the RC in the
desired range, using any kind of appropriate restraints. The boundary
biases of ABF are harmonic - if you start far away from the min or max
value, the excessive pulling on the system may have side-effects.

An ABF tutorial is in preparation. We will announce it on this mailing
list when it goes online - this should not take very long.

Jerome

On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
>
> Hi All,
>
> I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?
>
> I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.
>
> Jiancong
>
>



From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 11:28:17 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHSHjg020749;
	Mon, 14 Jan 2008 11:28:17 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHSGBx020748;
	Mon, 14 Jan 2008 11:28:16 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHSGTt020742;
	Mon, 14 Jan 2008 11:28:16 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHSGoN020741;
	Mon, 14 Jan 2008 11:28:16 -0600 (CST)
Received: from emroute3.ornl.gov (emroute3.ornl.gov [160.91.4.110])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHSBtA020727
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 11:28:11 -0600 (CST)
Received: from emroute3.ornl.gov ([127.0.0.1])
 by emroute3.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUN00G5N9KVUF@emroute3.ornl.gov> for namd-l@ks.uiuc.edu; Mon,
 14 Jan 2008 12:22:07 -0500 (EST)
Received: from CONVERSION-DAEMON.emroute3.ornl.gov by emroute3.ornl.gov
 (PMDF V6.3-x14 #31501) id <0JUN00H019KVA0@emroute3.ornl.gov>; Mon,
 14 Jan 2008 12:22:07 -0500 (EST)
Received: from ORNLEXCHANGE.ornl.gov (ornlexchange1.ornl.gov [160.91.1.20])
 by emroute3.ornl.gov (PMDF V6.3-x14 #31501)
 with ESMTP id <0JUN00FEY9KUYD@emroute3.ornl.gov>; Mon,
 14 Jan 2008 12:22:07 -0500 (EST)
Date: Mon, 14 Jan 2008 12:19:27 -0500
From: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: RE: namd-l: ABF question
To: Jerome Henin <jhenin@cmm.chem.upenn.edu>
Cc: namd-l@ks.uiuc.edu
Message-id: <E970EE66714B5741A9CF3C407B8605780504D3D5@ORNLEXCHANGE.ornl.gov>
MIME-version: 1.0
X-MIMEOLE: Produced By Microsoft Exchange V6.5
Content-type: text/plain; charset=iso-8859-1
Thread-Topic: namd-l: ABF question
Thread-Index: AchWz0qVuQQ2rYXiTBmf+yBYD/JbtgAAlMr7
Content-class: urn:content-classes:message
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
References: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
 <a61b1c250801090926y1f11b1ccrb51831d97f49038f@mail.gmail.com>
 <E970EE66714B5741A9CF3C407B8605780504D3D2@ORNLEXCHANGE.ornl.gov>
 <a61b1c250801140902x773efe2l4451cd05b2f117ae@mail.gmail.com>
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by halifax.ks.uiuc.edu id m0EHSBtA020728
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Jerome,

I am trying with smaller RC, for example, 1-2 A, and it seems the results are getting better. I'm also wondering how you prepare a well-equilibrated starting configuration for different ABF windows. Do you use SMD instead? Thanks.

Jiancong


-----Original Message-----
From: heninj@gmail.com on behalf of Jerome Henin
Sent: Mon 1/14/2008 12:02 PM
To: Xu, Jiancong
Cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: ABF question
 
Jiancong,
I'm afraid I cannot tell you much that has not been discussed on this
list before with other users, mostly to check for non-equilibrium
pulling effects and the influence of the fullSamples parameter. It
might be that your new starting configurations are not yet
well-equilibrated. It might be that there are other very slow degrees
of freedom in the system, interfering with your calculation.
Jerome

On Jan 14, 2008 11:14 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
>
> Hi Jerome and NAMD users,
>
> I started over with better configurations and it seems working now. However, the new problem is that the RC is not equally sampled. I've tried with different interval, initial configurations and bin width, and one of the borders is always oversampled than the rest. I would greatly appreciate any help and advice. Thanks much.
>
> Jiancong
>
>
>
>
>
> -----Original Message-----
> From: heninj@gmail.com on behalf of Jerome Henin
> Sent: Wed 1/9/2008 12:26 PM
> To: Xu, Jiancong
> Cc: namd-l@ks.uiuc.edu
> Subject: Re: namd-l: ABF question
>
>
> Hi Jiancong,
>
> It is best to prepare an equilibrated system with the RC in the
> desired range, using any kind of appropriate restraints. The boundary
> biases of ABF are harmonic - if you start far away from the min or max
> value, the excessive pulling on the system may have side-effects.
>
> An ABF tutorial is in preparation. We will announce it on this mailing
> list when it goes online - this should not take very long.
>
> Jerome
>
> On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
> >
> > Hi All,
> >
> > I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?
> >
> > I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.
> >
> > Jiancong
> >
> >
>
>



From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 11:41:00 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHf0Gs022920;
	Mon, 14 Jan 2008 11:41:00 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHf0VH022919;
	Mon, 14 Jan 2008 11:41:00 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHexPv022908;
	Mon, 14 Jan 2008 11:40:59 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EHexGR022901;
	Mon, 14 Jan 2008 11:40:59 -0600 (CST)
Received: from wr-out-0506.google.com (wr-out-0506.google.com [64.233.184.236])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EHenuT022891
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 11:40:50 -0600 (CST)
Received: by wr-out-0506.google.com with SMTP id c49so621079wra.21
        for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 09:40:49 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        bh=xKIFsUKnuzGNReO73vg8ZOJyBaWIRwgmwttpdygBd2c=;
        b=tyifuroEOQv61OGuWHdbVNFkMgV15Zf5JpT2k+p8OGi1ttKd0HCUYlWAJEKkkwuwFT3dSzmcEpsTiLATHsLUaCXTHliUaiKMEGUWdGxXD8IRznkMOC2O+uBQYXEqD0TrW1Ta4Utv4nNrZAJfvhz4QnhsbATr+mkz8hoBph5eKj8=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references:x-google-sender-auth;
        b=Nzu8whvwt+QMsKQleGngrjrWFEhy49abAYSbDEe+w/F+4xANGBUumX0BN08Hz6buLyZfdBzohOC3cHTGXmCVjTcNmNYEmFzzoO1RVT4jHoHLf+dr644HQe51U6yuzuGvmtmFeGDO8EvjaragJH1J9dr7TqQF+wKk891oWPJKGRg=
Received: by 10.150.195.21 with SMTP id s21mr2528591ybf.114.1200332449472;
        Mon, 14 Jan 2008 09:40:49 -0800 (PST)
Received: by 10.150.123.20 with HTTP; Mon, 14 Jan 2008 09:40:49 -0800 (PST)
Message-ID: <a61b1c250801140940k45029439t76a643bfe7b670a7@mail.gmail.com>
Date: Mon, 14 Jan 2008 12:40:49 -0500
From: "Jerome Henin" <jhenin@cmm.chem.upenn.edu>
To: "Xu, Jiancong" <xuj1@ornl.gov>
Subject: Re: namd-l: ABF question
Cc: namd-l@ks.uiuc.edu
In-Reply-To: <E970EE66714B5741A9CF3C407B8605780504D3D5@ORNLEXCHANGE.ornl.gov>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
References: <E970EE66714B5741A9CF3C407B8605780504D3C0@ORNLEXCHANGE.ornl.gov>
	 <a61b1c250801090926y1f11b1ccrb51831d97f49038f@mail.gmail.com>
	 <E970EE66714B5741A9CF3C407B8605780504D3D2@ORNLEXCHANGE.ornl.gov>
	 <a61b1c250801140902x773efe2l4451cd05b2f117ae@mail.gmail.com>
	 <E970EE66714B5741A9CF3C407B8605780504D3D5@ORNLEXCHANGE.ornl.gov>
X-Google-Sender-Auth: c3815abb2309b707
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Jiancong,
That's highly system-dependent. In some cases, picking a configuration
from one window to start the next one has worked well for me. Jerome

On Jan 14, 2008 12:19 PM, Xu, Jiancong <xuj1@ornl.gov> wrote:
> Jerome,
>
> I am trying with smaller RC, for example, 1-2 A, and it seems the results are getting better. I'm also wondering how you prepare a well-equilibrated starting configuration for different ABF windows. Do you use SMD instead? Thanks.
>
> Jiancong
>
>
> -----Original Message-----
> From: heninj@gmail.com on behalf of Jerome Henin
>
> Sent: Mon 1/14/2008 12:02 PM
> To: Xu, Jiancong
> Cc: namd-l@ks.uiuc.edu
> Subject: Re: namd-l: ABF question
>
> Jiancong,
> I'm afraid I cannot tell you much that has not been discussed on this
> list before with other users, mostly to check for non-equilibrium
> pulling effects and the influence of the fullSamples parameter. It
> might be that your new starting configurations are not yet
> well-equilibrated. It might be that there are other very slow degrees
> of freedom in the system, interfering with your calculation.
> Jerome
>
> On Jan 14, 2008 11:14 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
> >
> > Hi Jerome and NAMD users,
> >
> > I started over with better configurations and it seems working now. However, the new problem is that the RC is not equally sampled. I've tried with different interval, initial configurations and bin width, and one of the borders is always oversampled than the rest. I would greatly appreciate any help and advice. Thanks much.
> >
> > Jiancong
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: heninj@gmail.com on behalf of Jerome Henin
> > Sent: Wed 1/9/2008 12:26 PM
> > To: Xu, Jiancong
> > Cc: namd-l@ks.uiuc.edu
> > Subject: Re: namd-l: ABF question
> >
> >
> > Hi Jiancong,
> >
> > It is best to prepare an equilibrated system with the RC in the
> > desired range, using any kind of appropriate restraints. The boundary
> > biases of ABF are harmonic - if you start far away from the min or max
> > value, the excessive pulling on the system may have side-effects.
> >
> > An ABF tutorial is in preparation. We will announce it on this mailing
> > list when it goes online - this should not take very long.
> >
> > Jerome
> >
> > On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1@ornl.gov> wrote:
> > >
> > > Hi All,
> > >
> > > I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?
> > >
> > > I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.
> > >
> > > Jiancong
> > >
> > >
> >
> >
>
>


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 16:16:19 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EMGJfW007404;
	Mon, 14 Jan 2008 16:16:19 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EMGIGC007403;
	Mon, 14 Jan 2008 16:16:18 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EMGISm007391;
	Mon, 14 Jan 2008 16:16:18 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0EMGHsa007389;
	Mon, 14 Jan 2008 16:16:17 -0600 (CST)
Received: from hartman.uits.indiana.edu (hartman.uits.indiana.edu [129.79.1.194])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0EMGCMk007371
	(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 16:16:13 -0600 (CST)
Received: from spinner.uits.indiana.edu (spinner.uits.indiana.edu [129.79.1.139])
	by hartman.uits.indiana.edu (8.13.8/8.13.8/IU Messaging Team) with ESMTP id m0EMGBwu018103
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 17:16:12 -0500
Received: from localhost (spinner.uits.indiana.edu [127.0.0.1])
	by spinner.uits.indiana.edu (Postfix) with ESMTP id DE427101B6
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 17:16:11 -0500 (EST)
Received: from bl-chem-dione.chem.indiana.edu
	(bl-chem-dione.chem.indiana.edu [129.79.137.120]) by webmail.iu.edu (Horde
	MIME library) with HTTP; Mon, 14 Jan 2008 17:16:11 -0500
Message-ID: <20080114171611.fzls81byso08okgw@webmail.iu.edu>
Date: Mon, 14 Jan 2008 17:16:11 -0500
From: Yinglong Miao <yimiao@indiana.edu>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Characteristic time of atomic vibrations and collisions?
MIME-Version: 1.0
Content-Type: text/plain;
	charset=ISO-8859-1;
	format="flowed"
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
User-Agent: Internet Messaging Program (IMP) H3 (4.0.4)
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Dear NAMD users,

Here I have a quite fundamental question generally for MD. 1fs is the 
typical MD timestep we have been using for MD simulations. But as I 
searched for information about characteristic time of atomic vibrations 
and collisions, I found 10^12 for the atomic vibration frequency on one 
of the websites. This should indicate the characteristic time as 
10^(-12) s, which is 10^3 times larger than our MD timestep. It's right 
that the MD timestep needs to be smaller than the fastest vibrational 
frequency in the system, but how can this gap be so big? Or the number 
I found is not correct in some sense?

Thanks,
Long

--
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan 14 17:33:59 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0ENXxe3018692;
	Mon, 14 Jan 2008 17:33:59 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0ENXxcd018691;
	Mon, 14 Jan 2008 17:33:59 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0ENXwKM018683;
	Mon, 14 Jan 2008 17:33:58 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0ENXwgd018682;
	Mon, 14 Jan 2008 17:33:58 -0600 (CST)
Received: from biscayne-one-station.mit.edu (BISCAYNE-ONE-STATION.MIT.EDU [18.7.7.80])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0ENXqtr018648
	(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Mon, 14 Jan 2008 17:33:52 -0600 (CST)
Received: from outgoing.mit.edu (OUTGOING-AUTH.MIT.EDU [18.7.22.103])
	by biscayne-one-station.mit.edu (8.13.6/8.9.2) with ESMTP id m0ENXhXM016111;
	Mon, 14 Jan 2008 18:33:43 -0500 (EST)
Received: from [18.142.6.113] (FORD-THREE-SIXTY-EIGHT.MIT.EDU [18.142.6.113])
	(authenticated bits=0)
        (User authenticated as ovchinnv@ATHENA.MIT.EDU)
	by outgoing.mit.edu (8.13.6/8.12.4) with ESMTP id m0ENXgwF029121
	(version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT);
	Mon, 14 Jan 2008 18:33:43 -0500 (EST)
Subject: Re: namd-l: Characteristic time of atomic vibrations and
	collisions?
From: Victor Ovchinnikov <ovchinnv@MIT.EDU>
Reply-To: ovchinnv@MIT.EDU
To: Yinglong Miao <yimiao@indiana.edu>, namd-l@ks.uiuc.edu
In-Reply-To: <20080114171611.fzls81byso08okgw@webmail.iu.edu>
References: <20080114171611.fzls81byso08okgw@webmail.iu.edu>
Content-Type: text/plain
Organization: MIT
Date: Mon, 14 Jan 2008 18:33:42 -0500
Message-Id: <1200353622.3469.8.camel@ford-three-sixty-eight.mit.edu>
Mime-Version: 1.0
X-Mailer: Evolution 2.8.3 (2.8.3-2.fc6) 
Content-Transfer-Encoding: 7bit
X-Scanned-By: MIMEDefang 2.42
X-Spam-Flag: NO
X-Spam-Score: 0.00
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Long, 
You need to consider bond stretching frequencies, which will be of the
order of 2000 cm-1; this corresponds roughly to 17 fs per period.
Victor

On Mon, 2008-01-14 at 17:16 -0500, Yinglong Miao wrote:
> Dear NAMD users,
> 
> Here I have a quite fundamental question generally for MD. 1fs is the 
> typical MD timestep we have been using for MD simulations. But as I 
> searched for information about characteristic time of atomic vibrations 
> and collisions, I found 10^12 for the atomic vibration frequency on one 
> of the websites. This should indicate the characteristic time as 
> 10^(-12) s, which is 10^3 times larger than our MD timestep. It's right 
> that the MD timestep needs to be smaller than the fastest vibrational 
> frequency in the system, but how can this gap be so big? Or the number 
> I found is not correct in some sense?
> 
> Thanks,
> Long
> 
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981
> 


From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 15 10:06:36 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FG6aKU010570;
	Tue, 15 Jan 2008 10:06:36 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FG6asr010569;
	Tue, 15 Jan 2008 10:06:36 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FG6Zg6010564;
	Tue, 15 Jan 2008 10:06:35 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FG6ZZn010563;
	Tue, 15 Jan 2008 10:06:35 -0600 (CST)
Received: from hartman.uits.indiana.edu (hartman.uits.indiana.edu [129.79.1.194])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FG6Unk010554
	(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT)
	for <namd-l@ks.uiuc.edu>; Tue, 15 Jan 2008 10:06:30 -0600 (CST)
Received: from epona.uits.indiana.edu (epona.uits.indiana.edu [129.79.1.145])
	by hartman.uits.indiana.edu (8.13.8/8.13.8/IU Messaging Team) with ESMTP id m0FG6TAd020367;
	Tue, 15 Jan 2008 11:06:29 -0500
Received: from localhost (epona.uits.indiana.edu [127.0.0.1])
	by epona.uits.indiana.edu (Postfix) with ESMTP id 8B1FE100CA;
	Tue, 15 Jan 2008 11:06:29 -0500 (EST)
Received: from bl-chem-dione.chem.indiana.edu
	(bl-chem-dione.chem.indiana.edu [129.79.137.120]) by webmail.iu.edu (Horde
	MIME library) with HTTP; Tue, 15 Jan 2008 11:06:29 -0500
Message-ID: <20080115110629.sfwbband44gwgg0c@webmail.iu.edu>
Date: Tue, 15 Jan 2008 11:06:29 -0500
From: Yinglong Miao <yimiao@indiana.edu>
To: ovchinnv@MIT.EDU
Cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: Characteristic time of atomic vibrations and
	collisions?
References: <20080114171611.fzls81byso08okgw@webmail.iu.edu>
	<1200353622.3469.8.camel@ford-three-sixty-eight.mit.edu>
In-Reply-To: <1200353622.3469.8.camel@ford-three-sixty-eight.mit.edu>
MIME-Version: 1.0
Content-Type: text/plain;
	charset=ISO-8859-1;
	format="flowed"
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
User-Agent: Internet Messaging Program (IMP) H3 (4.0.4)
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

Victor,

Thanks for your reply. As I have found out, the atomic motions we want 
to simulate with MD have a spectrum of timescales, notably ranging from 
10^(-14) to 10^(-12) seconds. The fast vibrations of covalently bonded 
H atoms have periods from 9 to 10 fs and the MD timestep needs to be 
smaller.

Long

Quoting Victor Ovchinnikov <ovchinnv@MIT.EDU>:

> Long,
> You need to consider bond stretching frequencies, which will be of the
> order of 2000 cm-1; this corresponds roughly to 17 fs per period.
> Victor
>
> On Mon, 2008-01-14 at 17:16 -0500, Yinglong Miao wrote:
>> Dear NAMD users,
>>
>> Here I have a quite fundamental question generally for MD. 1fs is the
>> typical MD timestep we have been using for MD simulations. But as I
>> searched for information about characteristic time of atomic vibrations
>> and collisions, I found 10^12 for the atomic vibration frequency on one
>> of the websites. This should indicate the characteristic time as
>> 10^(-12) s, which is 10^3 times larger than our MD timestep. It's right
>> that the MD timestep needs to be smaller than the fastest vibrational
>> frequency in the system, but how can this gap be so big? Or the number
>> I found is not correct in some sense?
>>
>> Thanks,
>> Long
>>
>> --
>> Yinglong Miao
>> Ph.D. Candidate
>> Center for Cell and Virus Theory
>> Chemistry Department, Indiana University
>> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
>> Tel: 1-812-856-0981
>>
>
>



--
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981


From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 15 16:22:04 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FMM4k8011370;
	Tue, 15 Jan 2008 16:22:04 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FMM4fu011369;
	Tue, 15 Jan 2008 16:22:04 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FMM4kT011365;
	Tue, 15 Jan 2008 16:22:04 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FMM4PV011364;
	Tue, 15 Jan 2008 16:22:04 -0600 (CST)
Received: from py-out-1112.google.com (py-out-1112.google.com [64.233.166.176])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FMM1NA011357
	for <namd-l@ks.uiuc.edu>; Tue, 15 Jan 2008 16:22:01 -0600 (CST)
Received: by py-out-1112.google.com with SMTP id u77so22554pyb.15
        for <namd-l@ks.uiuc.edu>; Tue, 15 Jan 2008 14:22:00 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:mime-version:content-type:x-google-sender-auth;
        bh=jOzyhoecn28qACxc09GDNEi86KcdrUpEyr+1LFDGf5o=;
        b=ImZnk0ePLyxjfIFjMbtkcPTVNpphZtAwnyTm6Qho5/pLHtHZfI6NKUBn0rjzkUOZtagNluyyPF82ww9iyPnHM7KRbLhx65VOeIOVbt7xrjscrEwJ03y/GgtEgbhwLGOAAEdZMm7xUfqOhfnriNt0XsrkMF/hCVbZinA//+aCzOg=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:mime-version:content-type:x-google-sender-auth;
        b=bquM8uN06Tx9eznj+wofi3SuM+N5Agom+S31p3jQW/qBMFIdo4tVG3jDsGygWqsZ3M2GT9pR14ndz5O2acZ1prU0VqB2wzk0LI9ymUX/tMTMxScgblX9b1lNrqrixHCuw1UvyAieigT88QugWfjGaHaf8YzuDzMNuu+IyL7cpVI=
Received: by 10.65.81.10 with SMTP id i10mr18419200qbl.75.1200435718918;
        Tue, 15 Jan 2008 14:21:58 -0800 (PST)
Received: by 10.65.181.15 with HTTP; Tue, 15 Jan 2008 14:21:58 -0800 (PST)
Message-ID: <f7c18c850801151421g5ab13ad3l37caad01af728141@mail.gmail.com>
Date: Tue, 15 Jan 2008 15:21:58 -0700
From: "Lixia Jin Day" <ljin12@asu.edu>
To: namd-l@ks.uiuc.edu
Subject: namd-l: resonable dcdfreq
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_16889_2833418.1200435718900"
X-Google-Sender-Auth: d0316f3f002af9ca
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_16889_2833418.1200435718900
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear experts,

I used dcdfreq 500 (0.5fs) for my simulation before.  Now the data has been
collected over 1TB. I wander if it is ok to set it bigger, like 5000 or
10,000? What is a reasonable trojectory frequency?
Thanks!

------=_Part_16889_2833418.1200435718900
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

<br>Dear experts,<br>&nbsp;<br>I used dcdfreq 500 (0.5fs) for my simulation before.&nbsp; Now the data has been collected over 1TB. I wander if it is ok to set it bigger, like 5000 or 10,000? What is a reasonable trojectory frequency? 
<br>Thanks!<br>&nbsp;

------=_Part_16889_2833418.1200435718900--


From owner-namd-l@halifax.ks.uiuc.edu Tue Jan 15 17:09:46 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FN9kaL017072;
	Tue, 15 Jan 2008 17:09:46 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FN9kVn017071;
	Tue, 15 Jan 2008 17:09:46 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FN9jJ5017066;
	Tue, 15 Jan 2008 17:09:45 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0FN9jN1017065;
	Tue, 15 Jan 2008 17:09:45 -0600 (CST)
Received: from py-out-1112.google.com (py-out-1112.google.com [64.233.166.179])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0FN9gXQ017056
	for <namd-l@ks.uiuc.edu>; Tue, 15 Jan 2008 17:09:42 -0600 (CST)
Received: by py-out-1112.google.com with SMTP id u77so38798pyb.15
        for <namd-l@ks.uiuc.edu>; Tue, 15 Jan 2008 15:09:40 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-version:content-type;
        bh=BwYt6X/ceQanmH4Qr88GhJYf2OiQS/8EW1L0cAGDsWo=;
        b=uupiRX9RSXJeDtdDcjzcS0jWb2H2shwTOyRqzyQKJ9uK6ILou8LQEOP8gvUlfNsI3cl7C5BfH00iggVowgyWzKXuOVrkLppCOq3k1Nb7EAXEpd5/FrZCZroOR8WQlrx5mMOfase/FUK9TNDspmbsbFNj+7PAQ5+atAYbPIbp4Qw=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:mime-version:content-type;
        b=oAPmB+RDSDkTo0toqMM06BVfGl/QXLjvX9KjTc3TgwKJwolQO50bvbHWm5XwC0UuAFXF/zjbNrmLdUkeB3qkKkIkdbs0B46G2sYMAl0raTMrpPbXmwUikn8ubWlS2DMXl8uJCgsZahNK7q/sgiFprdzHT5eRU6NTcFU1i4LZKwg=
Received: by 10.140.251.1 with SMTP id y1mr20177rvh.292.1200438579620;
        Tue, 15 Jan 2008 15:09:39 -0800 (PST)
Received: by 10.140.134.3 with HTTP; Tue, 15 Jan 2008 15:09:39 -0800 (PST)
Message-ID: <57db477f0801151509y44254e31id47b90afc6ec6b04@mail.gmail.com>
Date: Tue, 15 Jan 2008 15:09:39 -0800
From: "Jianping Lin" <jianpingl@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Converting DCD file to XTC format
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_10770_3026694.1200438579615"
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_10770_3026694.1200438579615
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi,

Is there any scripts available to convert DCD fiile, psf file  into gromacs
XTC , tpr format?

Thanks

Jianping

------=_Part_10770_3026694.1200438579615
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Hi,<br><br>Is there any scripts available to convert DCD fiile, psf file&nbsp; into gromacs XTC , tpr format?<br><br>Thanks<br><br>Jianping<br>

------=_Part_10770_3026694.1200438579615--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 16 02:11:38 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0G8Bcgw007619;
	Wed, 16 Jan 2008 02:11:38 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0G8BcPL007618;
	Wed, 16 Jan 2008 02:11:38 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0G8Bb2j007614;
	Wed, 16 Jan 2008 02:11:37 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0G8BbXb007613;
	Wed, 16 Jan 2008 02:11:37 -0600 (CST)
Received: from unimix1.unimi.it (unimix1.unimi.it [159.149.10.81])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0G8BWSb007580
	for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 02:11:33 -0600 (CST)
X-AuditID: 9f950a51-aa5b9bb000000701-d7-478dbc2704c1
Received: from fara.unimi.net (unknown [172.24.3.21])
	by unimix1.unimi.it (Unimi Outbound) with ESMTP id 92D304E4005
	for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 09:11:19 +0100 (CET)
Received: from antares ([159.149.163.164])
 by ldap-s3.unimi.net (Sun Java System Messaging Server 6.2-8.04 (built Feb 28
 2007)) with SMTP id <0JUQ00IJS9EUOZ40@ldap-s3.unimi.net> for
 namd-l@ks.uiuc.edu; Wed, 16 Jan 2008 09:11:19 +0100 (CET)
Date: Wed, 16 Jan 2008 09:11:20 +0100
From: Alessandro Pedretti <alessandro.pedretti@unimi.it>
Subject: Re: namd-l: Converting DCD file to XTC format
To: Jianping Lin <jianpingl@gmail.com>, namd-l@ks.uiuc.edu
Message-id: <002301c85817$602f16d0$a4a3959f@antares>
MIME-version: 1.0
X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.3198
X-Mailer: Microsoft Outlook Express 6.00.2900.3138
Content-type: multipart/alternative;
 boundary="----=_NextPart_000_0020_01C8581F.C1EC52E0"
X-Priority: 3
X-MSMail-priority: Normal
References: <57db477f0801151509y44254e31id47b90afc6ec6b04@mail.gmail.com>
X-Brightmail-Tracker: AAAAAwiOHYYIji3nCI4zuA==
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

This is a multi-part message in MIME format.

------=_NextPart_000_0020_01C8581F.C1EC52E0
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Dear Jianping,
VEGA ZZ can perform the conversion from DCD to XTC. You can download it =
for free at http://www.ddl.unimi.it/vega/index2.htm .
For the conversion you need the coordinate file in PDB or another =
supported format. Follow these steps:
- If the PDB file has the same name of the DCD file (e.g. mymolecule.pdb =
and mymolecule.dcd), open directly the dcd file (File -> Open), =
otherwise open the PDB file, select Calculate -> Analysis and open the =
DCD file clicking on the open button.
- Select File -> Save trajectory, choose the trajectory format and the =
compression ratio, put the file name and click the save button.
At this time VEGA ZZ can't convert the PSF to tpr, but we are looking =
about the possibility to save the topology in that format directly.

Best regards

        Alessandro Pedretti


  ----- Original Message -----=20
  From: Jianping Lin=20
  To: namd-l@ks.uiuc.edu=20
  Sent: Wednesday, January 16, 2008 12:09 AM
  Subject: namd-l: Converting DCD file to XTC format


  Hi,

  Is there any scripts available to convert DCD fiile, psf file  into =
gromacs XTC , tpr format?

  Thanks

  Jianping

------=_NextPart_000_0020_01C8581F.C1EC52E0
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.6000.16587" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV>
<DIV>Dear Jianping,</DIV>
<DIV>VEGA ZZ can perform the conversion from DCD to XTC. You can =
download it for=20
free at <A=20
href=3D"http://www.ddl.unimi.it/vega/index2.htm">http://www.ddl.unimi.it/=
vega/index2.htm</A>&nbsp;.</DIV>
<DIV>For the conversion you need the coordinate file in PDB or=20
another&nbsp;supported format. Follow these steps:</DIV>
<DIV>- If the PDB file has the same name of the DCD file (e.g. =
mymolecule.pdb=20
and mymolecule.dcd), open directly the dcd file (File -&gt; Open), =
otherwise=20
open the PDB file, select Calculate -&gt; Analysis and open the DCD file =

clicking on the open button.</DIV>
<DIV>- Select File -&gt; Save trajectory, choose the trajectory format =
and the=20
compression ratio, put the file name and click the save button.</DIV>
<DIV>At this time VEGA ZZ can't convert the PSF to tpr, but we are =
looking about=20
the possibility to save the topology in that format directly.</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV>Best regards</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; Alessandro Pedretti</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></DIV>
<BLOCKQUOTE=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Djianpingl@gmail.com =
href=3D"mailto:jianpingl@gmail.com">Jianping=20
  Lin</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dnamd-l@ks.uiuc.edu=20
  href=3D"mailto:namd-l@ks.uiuc.edu">namd-l@ks.uiuc.edu</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Wednesday, January 16, =
2008 12:09=20
  AM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> namd-l: Converting DCD =
file to=20
  XTC format</DIV>
  <DIV><BR></DIV>Hi,<BR><BR>Is there any scripts available to convert =
DCD fiile,=20
  psf file&nbsp; into gromacs XTC , tpr=20
format?<BR><BR>Thanks<BR><BR>Jianping<BR></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_0020_01C8581F.C1EC52E0--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 16 11:04:19 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GH4JMn024251;
	Wed, 16 Jan 2008 11:04:19 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GH4J8k024250;
	Wed, 16 Jan 2008 11:04:19 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GH4IsV024246;
	Wed, 16 Jan 2008 11:04:18 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GH4IIb024245;
	Wed, 16 Jan 2008 11:04:18 -0600 (CST)
Received: from nz-out-0506.google.com (nz-out-0506.google.com [64.233.162.230])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GH4F7g024230
	for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 11:04:15 -0600 (CST)
Received: by nz-out-0506.google.com with SMTP id i1so259571nzh.39
        for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 09:04:15 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:sender:to:subject:mime-version:content-type:x-google-sender-auth;
        bh=8AHnaDsN/bHusuX7lbkP/wxSLG19mgIf5mqoJqVXXGY=;
        b=qWRcROZhsK0EhlhG5MBM9aze1uhCKbrTHJUqv7G9te/MMSBJPTc8lYcCSJGZBZxEu5V+Vef/qIAIApZv6a23+H+Q9TwiICz5lrFl52u2SX5znrxwhmBVM1bCpveD5Qc4/+A7Hgvr72D3FkB1skHyQC89mHseWSquo9N/F17FUbY=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:sender:to:subject:mime-version:content-type:x-google-sender-auth;
        b=C8d2ZoWud7zEPa1ybWucWFwqMAR+901QpCId35/qnWqYph+DktfWJwZxGs+9BrYvxbuVJMt25Fttscst/ESAOaFfzo9EWeSSFmUL2HDosn7zA72LXYcdHXbphAL1DSv5C6ogNaPbqZ6DEvGkj3VjacNruhofSizuRaAruYaTlBk=
Received: by 10.115.55.1 with SMTP id h1mr1168173wak.69.1200503054555;
        Wed, 16 Jan 2008 09:04:14 -0800 (PST)
Received: by 10.114.26.20 with HTTP; Wed, 16 Jan 2008 09:04:14 -0800 (PST)
Message-ID: <5407861b0801160904r67c226f7oe7f21b4cab05db5a@mail.gmail.com>
Date: Wed, 16 Jan 2008 12:04:14 -0500
From: "Seth Lilavivat" <sethl@gatech.edu>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Problems restarting an amber simulation
MIME-Version: 1.0
Content-Type: multipart/alternative; 
	boundary="----=_Part_23709_13086467.1200503054541"
X-Google-Sender-Auth: 0dff7fd8029994ba
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

------=_Part_23709_13086467.1200503054541
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear NAMD users,

I have a simulation that was stable under AMBER 8 and wanted to restart it
using NAMD. I assigned the Cell Basis Vectors according to page 13 of the
GROMACS 3.3 manual. I am relatively new to NAMD and am not sure why I am
getting the error below.  I have also experimented with the margin size and
get the same result.

ERROR: Constraint failure in RATTLE algorithm for atom 246!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 61!
ERROR: Constraint failure; simulation has become unstable.
FATAL ERROR: Periodic cell has become too small for original patch grid!

-------------------------------------------------------------------------------------------------------------------------------------

My config file is as follows:

rigidTolerance 0.0005  # Default is  0.00001
numsteps       5000  # Num of total steps
outputEnergies 50  # Energy output frequency
restartfreq    1000  # Restart file frequency
DCDfreq        100  # Trajectory file frequency
timestep       2  # in unit of fs
temperature    300  # Initial temp for velocity assignment
cutoff         10
switching      off  # Turn off the switching functions

PME            on  # Use PME for electrostatic calculation
# Orthogonal periodic box size
cellBasisVector1   66.119  22.040 -22.040
cellBasisVector2   0  7.666 3.833
cellBasisVector3   0  0  6.639
cellOrigin  29.845  29.562  29.864
PMEGridSizeX   70
PMEGridSizeY   70
PMEGridSizeZ   70

amber          on  # Specify this is AMBER force field
parmfile       telomere-aza3-wat.prmtop  # Input PARM file
ambercoor      md1.rst  # Input coordinate file
outputname     test-10ps  # Prefix of output files
exclude        scaled1-4
1-4scaling     0.833333  # =1/1.2, default is 1.0

Thank you for your help,
Seth

------=_Part_23709_13086467.1200503054541
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Dear NAMD users,<br>
<br>
I have a simulation that was stable under AMBER 8 and wanted to restart
it using NAMD. I assigned the Cell Basis Vectors according to page 13
of the GROMACS 3.3 manual. I am relatively new to NAMD and am not sure
why I am getting the error below.&nbsp; I have also experimented with
the margin size and get the same result.<br>
<br>
ERROR: Constraint failure in RATTLE algorithm for atom 246!<br>
ERROR: Constraint failure; simulation has become unstable.<br>
ERROR: Constraint failure in RATTLE algorithm for atom 5!<br>
ERROR: Constraint failure; simulation has become unstable.<br>
ERROR: Constraint failure in RATTLE algorithm for atom 61!<br>
ERROR: Constraint failure; simulation has become unstable.<br>
FATAL ERROR: Periodic cell has become too small for original patch grid!<br>
<br>
-------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
My config file is as follows:<br>
<br>
rigidTolerance 0.0005&nbsp; # Default is&nbsp; 0.00001<br>
numsteps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5000&nbsp; # Num of total steps<br>
outputEnergies 50&nbsp; # Energy output frequency<br>
restartfreq&nbsp;&nbsp;&nbsp; 1000&nbsp; # Restart file frequency<br>
DCDfreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 100&nbsp; # Trajectory file frequency<br>
timestep&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp; # in unit of fs<br>
temperature&nbsp;&nbsp;&nbsp; 300&nbsp; # Initial temp for velocity assignment<br>
cutoff&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10<br>
switching&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; off&nbsp; # Turn off the switching functions<br>
<br>
PME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on&nbsp; # Use PME for electrostatic calculation<br>
# Orthogonal periodic box size<br>
cellBasisVector1&nbsp;&nbsp; 66.119&nbsp; 22.040 -22.040<br>
cellBasisVector2&nbsp;&nbsp; 0&nbsp; 7.666 3.833<br>
cellBasisVector3&nbsp;&nbsp; 0&nbsp; 0&nbsp; 6.639<br>
cellOrigin&nbsp; 29.845&nbsp; 29.562&nbsp; 29.864<br>
PMEGridSizeX&nbsp;&nbsp; 70<br>
PMEGridSizeY&nbsp;&nbsp; 70<br>
PMEGridSizeZ&nbsp;&nbsp; 70<br>
<br>
amber&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on&nbsp; # Specify this is AMBER force field<br>
parmfile&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; telomere-aza3-wat.prmtop&nbsp; # Input PARM file<br>
ambercoor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; md1.rst&nbsp; # Input coordinate file<br>
outputname&nbsp;&nbsp;&nbsp;&nbsp; test-10ps&nbsp; # Prefix of output files<br>
exclude&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; scaled1-4<br>
1-4scaling&nbsp;&nbsp;&nbsp;&nbsp; 0.833333&nbsp; # =1/1.2, default is 1.0<br>
<br>
Thank you for your help,<br>
Seth <br>

------=_Part_23709_13086467.1200503054541--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 16 12:34:53 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GIYrUP009434;
	Wed, 16 Jan 2008 12:34:53 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GIYrbG009433;
	Wed, 16 Jan 2008 12:34:53 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GIYq6H009429;
	Wed, 16 Jan 2008 12:34:52 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GIYq9e009425;
	Wed, 16 Jan 2008 12:34:52 -0600 (CST)
Received: from bay0-omc1-s2.bay0.hotmail.com (bay0-omc1-s2.bay0.hotmail.com [65.54.246.74])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GIYkwY009405
	for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 12:34:47 -0600 (CST)
Received: from BAY122-W27 ([207.46.10.190]) by bay0-omc1-s2.bay0.hotmail.com with Microsoft SMTPSVC(6.0.3790.3959);
	 Wed, 16 Jan 2008 10:34:41 -0800
Message-ID: <BAY122-W27B6F2AA1BFDA2216B1895BF400@phx.gbl>
Content-Type: multipart/alternative;
	boundary="_0481e6d2-a50d-4c71-a60a-8bd914863b2c_"
X-Originating-IP: [72.234.209.206]
From: Irene Newhouse <einew@hotmail.com>
To: Seth Lilavivat <sethl@gatech.edu>, <namd-l@ks.uiuc.edu>
Subject: RE: namd-l: Problems restarting an amber simulation
Date: Wed, 16 Jan 2008 08:34:41 -1000
Importance: Normal
In-Reply-To: <5407861b0801160904r67c226f7oe7f21b4cab05db5a@mail.gmail.com>
References: <5407861b0801160904r67c226f7oe7f21b4cab05db5a@mail.gmail.com>
MIME-Version: 1.0
X-OriginalArrivalTime: 16 Jan 2008 18:34:41.0394 (UTC) FILETIME=[7513D520:01C8586E]
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

--_0481e6d2-a50d-4c71-a60a-8bd914863b2c_
Content-Type: text/plain; charset="Windows-1252"
Content-Transfer-Encoding: quoted-printable


While I haven't tried to switch a simulation between AMBER & NAMD - in fact=
, I'm not sure that that's such a hot idea - it complicates reproducibility=
 - I have run both AMBER-style & CHARMM-style simulations with NAMD. I find=
 that AMBER-style simulations are a lot less stable, and require more compl=
ex equilibration before they will run. One of the biggest bug-bears is tryi=
ng to get away with a 2fs time step. I suggest you drop to 1, adjust the fr=
equency of writing output so that you maintain your previous time interval =
per frame, & try again.
=20
Irene Newhouse


Date: Wed, 16 Jan 2008 12:04:14 -0500From: sethl@gatech.eduTo: namd-l@ks.ui=
uc.eduSubject: namd-l: Problems restarting an amber simulationDear NAMD use=
rs,I have a simulation that was stable under AMBER 8 and wanted to restart =
it using NAMD. I assigned the Cell Basis Vectors according to page 13 of th=
e GROMACS 3.3 manual. I am relatively new to NAMD and am not sure why I am =
getting the error below.  I have also experimented with the margin size and=
 get the same result.ERROR: Constraint failure in RATTLE algorithm for atom=
 246!ERROR: Constraint failure; simulation has become unstable.ERROR: Const=
raint failure in RATTLE algorithm for atom 5!ERROR: Constraint failure; sim=
ulation has become unstable.ERROR: Constraint failure in RATTLE algorithm f=
or atom 61!ERROR: Constraint failure; simulation has become unstable.FATAL =
ERROR: Periodic cell has become too small for original patch grid!---------=
---------------------------------------------------------------------------=
-------------------------------------------------My config file is as follo=
ws:rigidTolerance 0.0005  # Default is  0.00001numsteps       5000  # Num o=
f total stepsoutputEnergies 50  # Energy output frequencyrestartfreq    100=
0  # Restart file frequencyDCDfreq        100  # Trajectory file frequencyt=
imestep       2  # in unit of fstemperature    300  # Initial temp for velo=
city assignmentcutoff         10switching      off  # Turn off the switchin=
g functionsPME            on  # Use PME for electrostatic calculation# Orth=
ogonal periodic box sizecellBasisVector1   66.119  22.040 -22.040cellBasisV=
ector2   0  7.666 3.833cellBasisVector3   0  0  6.639cellOrigin  29.845  29=
.562  29.864PMEGridSizeX   70PMEGridSizeY   70PMEGridSizeZ   70amber       =
   on  # Specify this is AMBER force fieldparmfile       telomere-aza3-wat.=
prmtop  # Input PARM fileambercoor      md1.rst  # Input coordinate fileout=
putname     test-10ps  # Prefix of output filesexclude        scaled1-41-4s=
caling     0.833333  # =3D1/1.2, default is 1.0Thank you for your help,Seth=
=20
_________________________________________________________________
Make distant family not so distant with Windows Vista=AE + Windows Live=99.
http://www.microsoft.com/windows/digitallife/keepintouch.mspx?ocid=3DTXT_TA=
GLM_CPC_VideoChat_distantfamily_012008=

--_0481e6d2-a50d-4c71-a60a-8bd914863b2c_
Content-Type: text/html; charset="Windows-1252"
Content-Transfer-Encoding: quoted-printable

<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class=3D'hmmessage'>
While I haven't tried to switch a simulation between AMBER &amp; NAMD - in =
fact, I'm not sure that that's such a hot idea - it complicates reproducibi=
lity -&nbsp;I have run both AMBER-style &amp; CHARMM-style simulations with=
 NAMD. I find that AMBER-style simulations are a lot less stable, and requi=
re more complex equilibration before they will run. One of the biggest bug-=
bears is trying to get away with a 2fs time step. I suggest you drop to 1, =
adjust the frequency of writing output so that you maintain your previous t=
ime interval per frame, &amp; try again.<BR>
&nbsp;<BR>
Irene Newhouse<BR><BR><BR>
<BLOCKQUOTE>
<HR>
Date: Wed, 16 Jan 2008 12:04:14 -0500<BR>From: sethl@gatech.edu<BR>To: namd=
-l@ks.uiuc.edu<BR>Subject: namd-l: Problems restarting an amber simulation<=
BR><BR>Dear NAMD users,<BR><BR>I have a simulation that was stable under AM=
BER 8 and wanted to restart it using NAMD. I assigned the Cell Basis Vector=
s according to page 13 of the GROMACS 3.3 manual. I am relatively new to NA=
MD and am not sure why I am getting the error below.&nbsp; I have also expe=
rimented with the margin size and get the same result.<BR><BR>ERROR: Constr=
aint failure in RATTLE algorithm for atom 246!<BR>ERROR: Constraint failure=
; simulation has become unstable.<BR>ERROR: Constraint failure in RATTLE al=
gorithm for atom 5!<BR>ERROR: Constraint failure; simulation has become uns=
table.<BR>ERROR: Constraint failure in RATTLE algorithm for atom 61!<BR>ERR=
OR: Constraint failure; simulation has become unstable.<BR>FATAL ERROR: Per=
iodic cell has become too small for original patch grid!<BR><BR>-----------=
---------------------------------------------------------------------------=
-----------------------------------------------<BR><BR>My config file is as=
 follows:<BR><BR>rigidTolerance 0.0005&nbsp; # Default is&nbsp; 0.00001<BR>=
numsteps&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5000&nbsp; # Num of total step=
s<BR>outputEnergies 50&nbsp; # Energy output frequency<BR>restartfreq&nbsp;=
&nbsp;&nbsp; 1000&nbsp; # Restart file frequency<BR>DCDfreq&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp; 100&nbsp; # Trajectory file frequency<BR>timeste=
p&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp; # in unit of fs<BR>temperatur=
e&nbsp;&nbsp;&nbsp; 300&nbsp; # Initial temp for velocity assignment<BR>cut=
off&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10<BR>switching&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp; off&nbsp; # Turn off the switching functions<BR><BR>=
PME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on&nb=
sp; # Use PME for electrostatic calculation<BR># Orthogonal periodic box si=
ze<BR>cellBasisVector1&nbsp;&nbsp; 66.119&nbsp; 22.040 -22.040<BR>cellBasis=
Vector2&nbsp;&nbsp; 0&nbsp; 7.666 3.833<BR>cellBasisVector3&nbsp;&nbsp; 0&n=
bsp; 0&nbsp; 6.639<BR>cellOrigin&nbsp; 29.845&nbsp; 29.562&nbsp; 29.864<BR>=
PMEGridSizeX&nbsp;&nbsp; 70<BR>PMEGridSizeY&nbsp;&nbsp; 70<BR>PMEGridSizeZ&=
nbsp;&nbsp; 70<BR><BR>amber&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp; on&nbsp; # Specify this is AMBER force field<BR>parmfile&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp; telomere-aza3-wat.prmtop&nbsp; # Input PARM file<B=
R>ambercoor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; md1.rst&nbsp; # Input coordinate =
file<BR>outputname&nbsp;&nbsp;&nbsp;&nbsp; test-10ps&nbsp; # Prefix of outp=
ut files<BR>exclude&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; scaled1-4<BR>=
1-4scaling&nbsp;&nbsp;&nbsp;&nbsp; 0.833333&nbsp; # =3D1/1.2, default is 1.=
0<BR><BR>Thank you for your help,<BR>Seth <BR></BLOCKQUOTE><br /><hr />Make=
 distant family not so distant with Windows Vista=AE + Windows Live=99. <a =
href=3D'http://www.microsoft.com/windows/digitallife/keepintouch.mspx?ocid=
=3DTXT_TAGLM_CPC_VideoChat_distantfamily_012008' target=3D'_new'>Start now!=
</a></body>
</html>=

--_0481e6d2-a50d-4c71-a60a-8bd914863b2c_--


From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 16 14:35:59 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GKZxHq028288;
	Wed, 16 Jan 2008 14:35:59 -0600 (CST)
Received: (from majordom@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GKZx5w028287;
	Wed, 16 Jan 2008 14:35:59 -0600 (CST)
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to owner-namd-l@ks.uiuc.edu using -f
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GKZwcC028283;
	Wed, 16 Jan 2008 14:35:58 -0600 (CST)
Received: (from daemon@localhost)
	by halifax.ks.uiuc.edu (8.13.7+Sun/8.12.9/Submit) id m0GKZwqN028282;
	Wed, 16 Jan 2008 14:35:58 -0600 (CST)
Received: from rv-out-0910.google.com (rv-out-0910.google.com [209.85.198.191])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0GKZYrn028201
	for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 14:35:48 -0600 (CST)
Received: by rv-out-0910.google.com with SMTP id l15so309027rvb.24
        for <namd-l@ks.uiuc.edu>; Wed, 16 Jan 2008 12:35:30 -0800 (PST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
        d=gmail.com; s=gamma;
        h=domainkey-signature:received:received:message-id:date:from:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references;
        bh=48iNDaIRzk+ADrMz6wRKwoJOBkyetCFNJBlLL9BKQgs=;
        b=npU8fA7N+yjKK5XEXD3UXsdbcK9rat7J28t6FT1yEQeMZ7D8+PhivZCiaeSjl9BWz84st3gcNE6/Jo0F4hxlKYNtJlG/v2V+ZRkoUjk3V55HvrH64SkBFanrEZAtLgoZW01D/m0J9cAfuBhfqbTN6x690uSPL5iTAf4z8cW4u9s=
DomainKey-Signature: a=rsa-sha1; c=nofws;
        d=gmail.com; s=gamma;
        h=message-id:date:from:to:subject:cc:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references;
        b=MQCYvLbdhabI1SjSO6LrzCQ+04/ahSdrIwgL2RZvVpOj5iq/Xk1LxCFdXHafJFPaZVuPcoV3DDxJz0FXvG/9Q7kSV91/zmT1G/pEO/kakkNYAKw7dWqVrOMkXwFFpJiqmjWZ0iJeDqW6PTjAjSh380f+asg4xJBmM9+0HNHv+tU=
Received: by 10.141.161.6 with SMTP id n6mr861043rvo.201.1200515730517;
        Wed, 16 Jan 2008 12:35:30 -0800 (PST)
Received: by 10.140.248.15 with HTTP; Wed, 16 Jan 2008 12:35:30 -0800 (PST)
Message-ID: <914895270801161235h3fa3be37i600485093ec73561@mail.gmail.com>
Date: Wed, 16 Jan 2008 15:35:30 -0500
From: "Guanglei Cui" <amber.mail.archive@gmail.com>
To: "Seth Lilavivat" <sethl@gatech.edu>
Subject: Re: namd-l: Problems restarting an amber simulation
Cc: namd-l@ks.uiuc.edu
In-Reply-To: <5407861b0801160904r67c226f7oe7f21b4cab05db5a@mail.gmail.com>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
References: <5407861b0801160904r67c226f7oe7f21b4cab05db5a@mail.gmail.com>
Sender: owner-namd-l@ks.uiuc.edu
Precedence: bulk

I found it confusing that you tried to switch to NAMD from AMBER but
consulted Gromacs manual. Plus, if you don't make a velocity file out
of AMBER restart and include that in your NAMD input, you're not
really restarting the previous run. Anyway, if your box is
orthorhombic, you only specify the length in each dimension as
cellBasisVector, for example, 68.119 0 0. You can find box information
from the end of your AMBER restart. I hope this helps.

On Jan 16, 2008 12:04 PM, Seth Lilavivat <sethl@gatech.edu> wrote:
> Dear NAMD users,
>
>  I have a simulation that was stable under AMBER 8 and wanted to restart it
> using NAMD. I assigned the Cell Basis Vectors according to page 13 of the
> GROMACS 3.3 manual. I am relatively new to NAMD and am not sure why I am
> getting the error below.  I have also experimented with the margin size and
> get the same result.
>
>  ERROR: Constraint failure in RATTLE algorithm for atom 246!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 5!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 61!
>  ERROR: Constraint failure; simulation has become unstable.
>  FATAL ERROR: Periodic cell has become too small for original patch grid!
>
>
> -------------------------------------------------------------------------------------------------------------------------------------
>
>  My config file is as follows:
>
>  rigidTolerance 0.0005  # Default is  0.00001
>  numsteps       5000  # Num of total steps
>  outputEnergies 50  # Energy output frequency
>  restartfreq    1000  # Restart file frequency
>  DCDfreq        100  # Trajectory file frequency
>  timestep       2  # in unit of fs
>  temperature    300  # Initial temp for velocity assignment
>  cutoff         10
>  switching      off  # Turn off the switching functions
>
>  PME            on  # Use PME for electrostatic calculation
>  # Orthogonal periodic box size
>  cellBasisVector1   66.119  22.040 -22.040
>  cellBasisVector2   0  7.666 3.833
>  cellBasisVector3   0  0  6.639
>  cellOrigin  29.845  29.562  29.864
>  PMEGridSizeX   70
>  PMEGridSizeY   70
>  PMEGridSizeZ   70
>
>  amber          on  # Specify this is AMBER force field
>  parmfile       telomere-aza3-wat.prmtop  # Input PARM file
>  ambercoor      md1.rst  # Input coordinate file
>  outputname     test-10ps  # Prefix of output files
>  exclude        scaled1-4
>  1-4scaling     0.833333  # =1/1.2, default is 1.0
>
>  Thank you for your help,
>  Seth
>


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 17 06:44:07 2008
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])
	by halifax.ks.uiuc.edu (8.13.7/8.13.7) with ESMTP id m0HCi7AX027805;
	Thu, 17 Jan 2008 06:44:07 -0600 (CST)
Received: (from majord