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From: Arturas Ziemys <ziemys@chbmeng.ohio-state.edu>
Subject: namd-l: Tcl_BC: [nexatom] twice in script
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Hi,

I am using Tcl BC script. In the first loop with [nextatom] I calculate property, and with second repeated loop I calculated force depending on the property I have calculated in the first loop of atoms:

tclBCScript {
  .....
  while {[nextatom]} {
    <analyze coords>
  }

  while {[nextatom]} {
    <apply force>
    <do output to log file>
  }
}

However, I am not able 'print' or 'puts <file>' any information. I tried to output some data to variable and pass it for printing outside the second [nextatom] loop, but it seems that I'm also not able to reassign variable to outside of loop defined variable. It looks like second call of [nextatom] loop  is terminated at the beginning?

Is any limitation of how many times I can invoke [nextatom] loop ?

How can I store any variable or data to read in the next step (without writing/reading file) ?

Arturas





From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  2 15:45:30 2007
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Date: Tue, 02 Jan 2007 16:45:23 -0500
To: namd-l@ks.uiuc.edu
From: Kramer Campen <campen@geosc.psu.edu>
Subject: namd-l: Free Energy of Conformation Change Units
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Hey Folks:

A, probably, obvious question...

In the Free Energy of Conformation Change output (either through 
thermodynamic integration or slow growth) what units does the free energy 
have?  I'm guessing it's kcal/mol (like the rest of the NAMD output) but 
would appreciate a confirmation.

Thanks in advance.

Kramer


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Date: Fri, 5 Jan 2007 21:05:40 +0800
From: laura <jinboting@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: SPC/E water model
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Hello
   I want to compute diffusivity of molecular by using SPC/E water models .
How I  solvate molecular  by VMD in SPC/E models?   And where I can get
topology and parameter files which  include SPC/E  water model?  Thank you
for any help!

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<div>Hello</div>
<div>&nbsp;&nbsp; I want to compute diffusivity of molecular by using SPC/E water models . How I&nbsp; solvate molecular&nbsp; by VMD in SPC/E models?&nbsp;&nbsp; And where I can get topology and parameter files which&nbsp;&nbsp;include SPC/E&nbsp; water model?&nbsp; Thank you for any help!
<br> </div>

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Date: Fri, 5 Jan 2007 12:31:18 -0600
From: "Nitin Bhardwaj" <nbhardwaj@gmail.com>
To: namd-l@ks.uiuc.edu, vmd-l@ks.uiuc.edu
Subject: namd-l: "Not all atoms have unique coordinates"
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Dear Namd users,
     I have a strange problem in my simulation of a single lipid
molecule. During minimization, I keep getting this warning "Not all atoms
have unique coordinates". The simulation stops as soon as production run
starts with the message:

Reason: 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.

I tried increasing the magint but no help. I check my molecule and
everything is fine with it. There are no atoms overlapping.

Its NAMD2.6 on linux.

Has anyone seen this problem before? Is there any way to go around this?

Thanks a lot in advance.
Rgds,
Nitin

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<div>Dear Namd users,</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp; I have a strange problem in my simulation of a single lipid molecule.&nbsp;During minimization,&nbsp;I keep getting this warning &quot;Not all atoms have unique coordinates&quot;. The simulation stops as soon as&nbsp;production run starts with the message:
</div>
<div>&nbsp;</div>
<div>Reason: 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>
&nbsp;</div>
<div>I tried increasing the magint but no help. I check my molecule and everything is fine with it. There are no atoms overlapping. </div>
<div>&nbsp;</div>
<div>Its NAMD2.6 on linux.</div>
<div>&nbsp;</div>
<div>Has anyone seen this problem before? Is there any way to go around this?</div>
<div>&nbsp;</div>
<div>Thanks a lot in advance.</div>
<div>Rgds,</div>
<div>Nitin<br clear="all"></div>

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Dear NAMD users,

I have just installed a new cluster with 9 servers having 2 Intel Xeon
Dual-core 3.0GHz and 4GB RAM each. I am using the Open SuSE 10.2 OS. I also
tried with the SuSE Linux Enterprise Server 10 but nothing changed.

I tried to submit a very simple NAMD job that I was used to do and I found
a problem. I do not know why, but when I run the job locally, it runs okay,
but if I try to run using 2 or more servers (no matter the number of
processes submitted, e.g. ++p 6 or ++p 10) it freezes when NAMD start to
allocate memory. I tried to change the servers to see it was something
about a particular server, but I still have the problem no matter the
server or the number of them that I use. I can access using rsh all the
servers without a password successfully.

Charmrun> charmrun started...
Charmrun> using /home/cluster/Protein/namd/nodelist as nodesfile
Charmrun> rsh (lbbc02:0) started
Charmrun> rsh (lbbc02:1) started
Charmrun> rsh (lbbc03:2) started
Charmrun> rsh (lbbc03:3) started
Charmrun> node programs all started
Charmrun rsh(lbbc03.2)> remote responding...
Charmrun rsh(lbbc02.1)> starting node-program...
Charmrun rsh(lbbc02.1)> rsh phase successful.
Charmrun rsh(lbbc03.3)> starting node-program...
Charmrun rsh(lbbc03.3)> rsh phase successful.
Charmrun rsh(lbbc03.2)> starting node-program...
Charmrun rsh(lbbc03.2)> rsh phase successful.
Charmrun> node programs all connected
Charmrun> adding client 0: "lbbc02", IP:10.46.11.53
Charmrun> adding client 1: "lbbc02", IP:10.46.11.53
Charmrun> adding client 2: "lbbc03", IP:127.0.0.1
Charmrun> adding client 3: "lbbc03", IP:127.0.0.1
Charmrun> Charmrun = lbbc03, port = 50639
Charmrun> Sending "0 lbbc03 50639 25145 0" to client 0.
Charmrun> find the node program "/home/cluster/Protein/namd/namd2" at
"/home/cluster/Protein/namd" for 0.
Charmrun> Starting rsh lbbc02 -l cluster /bin/sh -f
Charmrun> Sending "1 lbbc03 50639 25145 0" to client 1.
Charmrun> find the node program "/home/cluster/Protein/namd/namd2" at
"/home/cluster/Protein/namd" for 1.
Charmrun> Starting rsh lbbc02 -l cluster /bin/sh -f
Charmrun> Sending "2 lbbc03 50639 25145 0" to client 2.
Charmrun> find the node program "/home/cluster/Protein/namd/namd2" at
"/home/cluster/Protein/namd" for 2.
Charmrun> Starting rsh lbbc03 -l cluster /bin/sh -f
Charmrun> Sending "3 lbbc03 50639 25145 0" to client 3.
Charmrun> find the node program "/home/cluster/Protein/namd/namd2" at
"/home/cluster/Protein/namd" for 3.
Charmrun> Starting rsh lbbc03 -l cluster /bin/sh -f
Charmrun> waiting for rsh (lbbc02:0), pid 25146
Charmrun> waiting for rsh (lbbc02:1), pid 25147
Charmrun> waiting for rsh (lbbc03:2), pid 25148
Charmrun> waiting for rsh (lbbc03:3), pid 25150
Charmrun> Waiting for 0-th client to connect.
Charmrun> client 0 connected (IP=10.46.11.53 data_port=32785)
Charmrun> Waiting for 1-th client to connect.
Charmrun> client 1 connected (IP=10.46.11.53 data_port=32786)
Charmrun> Waiting for 2-th client to connect.
Charmrun> client 2 connected (IP=127.0.0.1 data_port=32787)
Charmrun> Waiting for 3-th client to connect.
Charmrun> client 3 connected (IP=127.0.0.1 data_port=32788)
Charmrun> All clients connected.
Charmrun> IP tables sent.
Info: NAMD 2.6 for Linux-amd64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD  2.6  Linux-amd64  4    lbbc02  cluster
Info: Running on 4 processors.
Info: 7608 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to /home/cluster/Protein/namd/protocols
Info: Configuration file is MD-2ns.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        10
Info: PERIODIC CELL BASIS 1  67.1 0 0
Info: PERIODIC CELL BASIS 2  0 72.6 0
Info: PERIODIC CELL BASIS 3  0 0 70.3
Info: PERIODIC CELL CENTER   -8.4 -36.2 -28.8
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: MIN ATOMS PER PATCH    100
Info: INITIAL TEMPERATURE    310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           ../output/protein_wb-MD-2ns.dcd
Info: DCD FREQUENCY          1000
Info: DCD FIRST STEP         1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           ../output/protein_wb-MD-2ns.xst
Info: XST FREQUENCY          1000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        ../output/protein_wb-MD-2ns
Info: RESTART FILENAME       ../output/protein_wb-MD-2ns.restart
Info: RESTART FREQUENCY      1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      13.5
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 2.5
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        18.5
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    100
Info: PRESSURE OUTPUT STEPS  100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1.01325 BAR
Info:     OSCILLATION PERIOD IS 100 FS
Info:             DECAY TIME IS 50 FS
Info:     PISTON TEMPERATURE IS 310 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         72 75 72
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1168020387
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ../output/protein_wb-MM.coor
Info: STRUCTURE FILE         ../procdata/protein_wb.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             ../param/par_all22_prot.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 138 BONDS
Info: 341 ANGLES
Info: 443 DIHEDRAL
Info: 43 IMPROPER
Info: 0 CROSSTERM
Info: 65 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 31728 ATOMS
Info: 21797 BONDS
Info: 13406 ANGLES
Info: 5106 DIHEDRALS
Info: 297 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 30800 RIGID BONDS
Info: 64384 DEGREES OF FREEDOM
Info: 10877 HYDROGEN GROUPS
Info: TOTAL MASS = 192513 amu
Info: TOTAL CHARGE = 8 e
Info: *****************************
Info: Entering startup phase 0 with 13268 kB of memory in use.

When NAMD gets here it cannot go forward. The job is still there and if I
let it for hours, it will not die. All the processors are free and the
/var/log/messages do not show any error.

Any help is appreciated.

Regards,

Fabio Passetti


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Subject: RE: namd-l: "Not all atoms have unique coordinates"
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Thread-Topic: namd-l: "Not all atoms have unique coordinates"
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From: "Ana Celia Araujo Vila Verde" <avilaverde@engr.psu.edu>
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Hi,
=20
Are you running NPT?  I don't think you should, for a single molecule.  =
you should run NVT (just comment out all the lines related to the =
pressure control in your configuration file for that).  Also, make sure =
that cellBasisVectorX(Y,Z) is made 1) sufficiently bigger than your =
molecule, so that atoms from the original molecule don't overlap with =
atoms from the periodic image of the molecule and 2) bigger than your =
cutoff distance, so that the molecule does not interact with its image.
=20
Let us know how it works.
=20
Hope it helps,
=20
Ana
=20
=20
_________________________________
Ana C=E9lia Ara=FAjo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA
=20
 <http://www.gfct.fisica.uminho.pt/Members/acvv> =20
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
avilaverde@engr.psu.edu
http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
http://www.gfct.fisica.uminho.pt/Members/acvv
_________________________________


-----Original Message-----
From: owner-namd-l@ks.uiuc.edu [mailto:owner-namd-l@ks.uiuc.edu] On =
Behalf Of Nitin Bhardwaj
Sent: Friday, January 05, 2007 1:31 PM
To: namd-l@ks.uiuc.edu; vmd-l@ks.uiuc.edu
Subject: namd-l: "Not all atoms have unique coordinates"


Dear Namd users,
     I have a strange problem in my simulation of a single lipid =
molecule. During minimization, I keep getting this warning "Not all =
atoms have unique coordinates". The simulation stops as soon as =
production run starts with the message:=20
=20
Reason: 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.
=20
I tried increasing the magint but no help. I check my molecule and =
everything is fine with it. There are no atoms overlapping.=20
=20
Its NAMD2.6 on linux.
=20
Has anyone seen this problem before? Is there any way to go around this?
=20
Thanks a lot in advance.
Rgds,
Nitin



------_=_NextPart_001_01C730FB.7999FD6E
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<TITLE>Message</TITLE>

<META content=3D"MSHTML 6.00.2900.3020" name=3DGENERATOR></HEAD>
<BODY>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN =
class=3D700345418-05012007>Are=20
you running NPT?&nbsp; I don't think you should, for a single =
molecule.&nbsp;=20
you should run NVT (just comment out all the lines related to the =
pressure=20
control in your configuration file for that).&nbsp; Also, make sure that =

cellBasisVectorX(Y,Z) is made 1) sufficiently bigger than your molecule, =
so that=20
atoms from the original molecule don't overlap with atoms from the =
periodic=20
image of the molecule and 2) bigger than your cutoff distance, so that =
the=20
molecule does not interact with its image.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN =
class=3D700345418-05012007>Let us=20
know how it works.</SPAN></FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN =
class=3D700345418-05012007>Hope=20
it helps,</SPAN></FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2><SPAN=20
class=3D700345418-05012007>Ana</SPAN></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV align=3Dleft><FONT face=3DArial=20
size=3D2>_________________________________</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Ana C=E9lia Ara=FAjo Vila =
Verde</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Penn State =
University</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Department of Chemical=20
Engineering</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Fenske =
Laboratory<BR>University Park, PA=20
16802</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>USA</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2><A=20
href=3D"http://www.gfct.fisica.uminho.pt/Members/acvv"></A></FONT>&nbsp;<=
/DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Phone: +(1) <!-- =
InstanceBeginEditable name=3D"EditRegion6" -->(814) 863-2879<BR>Fax: =
+(1) <!-- InstanceBeginEditable name=3D"EditRegion6a" -->(814) =
865-7846</FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2><A=20
href=3D"mailto:avilaverde@engr.psu.edu">avilaverde@engr.psu.edu</A></FONT=
></DIV>
<DIV align=3Dleft>
<DIV align=3Dleft><FONT face=3DArial size=3D2><A=20
href=3D"http://www.che.psu.edu/Faculty/JMaranas/group/avv.html">http://ww=
w.che.psu.edu/Faculty/JMaranas/group/avv.html</A></FONT></DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2><A=20
href=3D"http://www.gfct.fisica.uminho.pt/Members/acvv">http://www.gfct.fi=
sica.uminho.pt/Members/acvv</A></FONT></DIV></DIV>
<DIV align=3Dleft><FONT face=3DArial =
size=3D2>_________________________________<!-- InstanceEndEditable =
--><BR></DIV></FONT>
<BLOCKQUOTE dir=3Dltr style=3D"MARGIN-RIGHT: 0px">
  <DIV></DIV>
  <DIV class=3DOutlookMessageHeader lang=3Den-us dir=3Dltr =
align=3Dleft><FONT=20
  face=3DTahoma size=3D2>-----Original Message-----<BR><B>From:</B>=20
  owner-namd-l@ks.uiuc.edu [mailto:owner-namd-l@ks.uiuc.edu] <B>On =
Behalf Of=20
  </B>Nitin Bhardwaj<BR><B>Sent:</B> Friday, January 05, 2007 1:31=20
  PM<BR><B>To:</B> namd-l@ks.uiuc.edu; =
vmd-l@ks.uiuc.edu<BR><B>Subject:</B>=20
  namd-l: "Not all atoms have unique coordinates"<BR><BR></FONT></DIV>
  <DIV>Dear Namd users,</DIV>
  <DIV>&nbsp;&nbsp;&nbsp;&nbsp; I have a strange problem in my =
simulation of a=20
  single lipid molecule.&nbsp;During minimization,&nbsp;I keep getting =
this=20
  warning "Not all atoms have unique coordinates". The simulation stops =
as soon=20
  as&nbsp;production run starts with the message: </DIV>
  <DIV>&nbsp;</DIV>
  <DIV>Reason: FATAL ERROR: Periodic cell has become too small for =
original=20
  patch grid!<BR>Possible solutions are to restart from a recent=20
  checkpoint,<BR>increase margin, or disable useFlexibleCell for liquid=20
  simulation.<BR>&nbsp;</DIV>
  <DIV>I tried increasing the magint but no help. I check my molecule =
and=20
  everything is fine with it. There are no atoms overlapping. </DIV>
  <DIV>&nbsp;</DIV>
  <DIV>Its NAMD2.6 on linux.</DIV>
  <DIV>&nbsp;</DIV>
  <DIV>Has anyone seen this problem before? Is there any way to go =
around=20
  this?</DIV>
  <DIV>&nbsp;</DIV>
  <DIV>Thanks a lot in advance.</DIV>
  <DIV>Rgds,</DIV>
  <DIV>Nitin<BR clear=3Dall></DIV></BLOCKQUOTE></BODY></HTML>

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From owner-namd-l@halifax.ks.uiuc.edu Fri Jan  5 13:16:47 2007
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From: "Neelanjana Sengupta" <senguptan@gmail.com>
To: "Nitin Bhardwaj" <nbhardwaj@gmail.com>, NAMD <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: "Not all atoms have unique coordinates"
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It looks like you have some bad contacts between atoms, which remain even
after minimization. Did the "production run" go forward by even a few steps?
If so, you can try re-starting the simulation from wherever it
stops...sometimes that solves the problem.
Otherwise, you may have to re-check your starting conformations.

Best,
Neelanjana

On 1/5/07, Nitin Bhardwaj <nbhardwaj@gmail.com> wrote:
>
> Dear Namd users,
>      I have a strange problem in my simulation of a single lipid
> molecule. During minimization, I keep getting this warning "Not all atoms
> have unique coordinates". The simulation stops as soon as production run
> starts with the message:
>
> Reason: 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.
>
> I tried increasing the magint but no help. I check my molecule and
> everything is fine with it. There are no atoms overlapping.
>
> Its NAMD2.6 on linux.
>
> Has anyone seen this problem before? Is there any way to go around this?
>
> Thanks a lot in advance.
> Rgds,
> Nitin
>



-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta@uci.edu
****************************************

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It looks like you have some bad contacts between atoms, which remain even after minimization. Did the &quot;production run&quot; go forward by even a few steps? If so, you can try re-starting the simulation from wherever it stops...sometimes that solves the problem.
<br>Otherwise, you may have to re-check your starting conformations.<br><br>Best,<br>Neelanjana<br><br><div><span class="gmail_quote">On 1/5/07, <b class="gmail_sendername">Nitin Bhardwaj</b> &lt;<a href="mailto:nbhardwaj@gmail.com">
nbhardwaj@gmail.com</a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Dear Namd users,</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp; I have a strange problem in my simulation of a single lipid molecule.&nbsp;During minimization,&nbsp;I keep getting this warning &quot;Not all atoms have unique coordinates&quot;. The simulation stops as soon as&nbsp;production run starts with the message:
</div>
<div>&nbsp;</div>
<div>Reason: 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>

&nbsp;</div>
<div>I tried increasing the magint but no help. I check my molecule and everything is fine with it. There are no atoms overlapping. </div>
<div>&nbsp;</div>
<div>Its NAMD2.6 on linux.</div>
<div>&nbsp;</div>
<div>Has anyone seen this problem before? Is there any way to go around this?</div>
<div>&nbsp;</div>
<div>Thanks a lot in advance.</div>
<div>Rgds,</div><span class="sg">
<div>Nitin<br clear="all"></div>

</span></blockquote></div><br><br clear="all"><br>-- <br>****************************************<br>Neelanjana Sengupta, PhD student<br>Dept. of Chemistry<br>Univ. of California-Irvine<br>Irvine, CA 92697<br>USA<br>Phone: 1-949-824 9921
<br>email: <a href="mailto:sengupta@uci.edu">sengupta@uci.edu</a><br>****************************************

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From owner-namd-l@halifax.ks.uiuc.edu Fri Jan  5 13:39:18 2007
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Hi Nitin,

Very likely your psf and/or pdb files have some error. You should NOT have 
a "Not all atoms have unique coordinates" message.

How are you setting up periodic boundary conditions for a single lipid 
molecule?

Marcos

On Fri, 5 Jan 2007, Nitin Bhardwaj wrote:

> Dear Namd users,
>    I have a strange problem in my simulation of a single lipid
> molecule. During minimization, I keep getting this warning "Not all atoms
> have unique coordinates". The simulation stops as soon as production run
> starts with the message:
>
> Reason: 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.
>
> I tried increasing the magint but no help. I check my molecule and
> everything is fine with it. There are no atoms overlapping.
>
> Its NAMD2.6 on linux.
>
> Has anyone seen this problem before? Is there any way to go around this?
>
> Thanks a lot in advance.
> Rgds,
> Nitin
>

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Date: Mon, 8 Jan 2007 16:36:07 +0530 (IST)
From: arijit_r@chem.iitkgp.ernet.in
To: namd-l@ks.uiuc.edu
Subject: namd-l: topology of carbon dioxide compatible with Charmm
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Dear NAMD users,
     Does anybody has prepared topology file for carbon dioxide that
can be used with charmm?
    If yes, can he /she can provide me that.
           Thank you,
                                   Arijit



From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  8 05:26:57 2007
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Date: Mon, 8 Jan 2007 13:26:54 +0200
From: "Idit Buch" <iditbuch@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: ligand parameterization
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Hi all.
I am working with CHARMM FF and trying to run a small ligand inside a
protein.
I have a problem with the new parameters.
The problem is maintaing a cp3 configuration of a carbon on a ring. The
species is like

R--------------------R
 \       H           /
  \       |          /
  N ----C*-----C
          |
         O
          |
         H
And I am using improper parameters  C* H O C and C* H O N ,but it doesnt
solve the C* cp3 problem.
Can any of you have any experience with such a problem?


Many thanks.

Idit Buch

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<div><font face="Arial" size="2">Hi all.</font></div>
<div><font face="Arial" size="2">I am working with CHARMM FF and trying to run a small ligand inside a protein.</font></div>
<div><font face="Arial" size="2">I have a problem with the new parameters. </font></div>
<div><font face="Arial" size="2">The problem is maintaing a cp3 configuration of a carbon on a ring. The species is like</font></div>
<div><font face="Arial" size="2"></font>&nbsp;</div>
<div><font face="Arial" size="2">R--------------------R</font></div>
<div><font face="Arial" size="2">&nbsp;\&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /</font></div>
<div><font face="Arial" size="2">&nbsp; \&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /</font></div>
<div><font face="Arial" size="2">&nbsp; N&nbsp;----C*-----C</font></div>
<div><font face="Arial" size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |</font></div>
<div><font face="Arial" size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O</font></div>
<div><font face="Arial" size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |</font></div>
<div><font face="Arial" size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; H</font></div>
<div><font face="Arial" size="2">And I am using improper parameters&nbsp; C* H O C and C* H O N ,but it doesnt solve the C* cp3 problem.</font></div>
<div><font face="Arial" size="2">Can any of you have any experience with such a problem?</font></div>
<div><font face="Arial" size="2"></font>&nbsp;</div>
<div><font face="Arial" size="2"></font>&nbsp;</div>
<div><font face="Arial" size="2">Many thanks.</font></div>
<div><font size="2"></font>&nbsp;</div>
<div><font size="2">Idit Buch</font></div>
<div><font size="2"></font>&nbsp;</div>

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From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  8 11:27:28 2007
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From: JC Gumbart <gumbart@ks.uiuc.edu>
Subject: Re: namd-l: topology of carbon dioxide compatible with Charmm
Date: Mon, 8 Jan 2007 11:27:20 -0600
To: arijit_r@chem.iitkgp.ernet.in
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If you download the full charmm set, you'll find it in stream/ 
toppar_all22_prot_heme.str


On Jan 8, 2007, at 5:06 AM, arijit_r@chem.iitkgp.ernet.in wrote:

> Dear NAMD users,
>     Does anybody has prepared topology file for carbon dioxide that
> can be used with charmm?
>    If yes, can he /she can provide me that.
>           Thank you,
>                                   Arijit
>


From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  8 11:56:11 2007
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Date: Mon, 8 Jan 2007 23:26:26 +0530 (IST)
From: arijit_r@chem.iitkgp.ernet.in
To: JC Gumbart <gumbart@ks.uiuc.edu>
cc: namd-l@ks.uiuc.edu
Subject: Re: namd-l: topology of carbon dioxide compatible with Charmm
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Dear Gumbart,
    Thank you very much. I got it.
                                     Arijit

On Mon, 8 Jan 2007, JC Gumbart wrote:

> If you download the full charmm set, you'll find it in 
> stream/toppar_all22_prot_heme.str
>
>
> On Jan 8, 2007, at 5:06 AM, arijit_r@chem.iitkgp.ernet.in wrote:
>
>> Dear NAMD users,
>>    Does anybody has prepared topology file for carbon dioxide that
>> can be used with charmm?
>>   If yes, can he /she can provide me that.
>>          Thank you,
>>                                  Arijit
>> 
>



From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  8 12:11:03 2007
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Date: Mon, 08 Jan 2007 13:11:02 -0500
To: namd-l@ks.uiuc.edu
From: Kramer Campen <campen@geosc.psu.edu>
Subject: namd-l: Thermodynamic Integration (free energy of conformation change)
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Hey Folks:

I have a quick question about the standard MCTI block (as written in the 
NAMD user's guide) that I thought others might be able to answer...

A section of the MCTI input might look like....

mcti {
   task = stepup
   equiltime = 10 ps
   accumtime = 10 ps
   numsteps = 36
   print = 1 ps
}

In this arrangement the free energy will be printed 10 times at each value 
of lambda (at ps 1, 2, 3, etc...).  My question is whether the value of 
free energy printed at ps 2 is based on the simulation data from 1-2 ps or 
from 0-2 ps?

I suspect it makes sense to average over the entire length of the accumtime 
but the documentation is a bit scanty on this point.

Thanks in advance for any insight.

Kramer Campen


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Date: Mon, 8 Jan 2007 12:35:07 -0600
From: "Rima Chaudhuri" <rima.chaudhuri@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: Protein, ligand, ion out of the water box.
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Hi All,
I am trying to simulate a protein with a calcium ion and ligand attached
using Amber forcefield in namd for 1ns, in two instances.
Case1: Simulating the protein with Calcium attached in 10A water box
Case2: Simulate the protein complex with inhibitor in a 10A water box

In both the cases, right from frame 0, (I minimize for 1000 steps) the
protein comes out of the water box and tethers to one edge, while the
calcium ion and ligand comes out and tethers themselves to two other edges
of the box. In other words they are partially immersed (just anchorched) to
the water box on 3 different sides. Initially i thought it might be the
parameters of Ca or ligand that is causing this, so I tried simulating the
protein alone w/o Ca2+ even, it does the same thing, the protein comes out
and even translates to another edge of the box after some 1000 frames
randomly.
The following is my .config file. Any guidance will be much appreciated.

amber           yes
parmfile        fxa_wat_ca.prmtop
ambercoor       fxa_wat_ca.inpcrd



set temperature     310
set outputname      outFxa_ca

firsttimestep       0


#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm      off
temperature             0
reassignFreq         1000
reassignTemp        25
reassignIncr          25
reassignHold        310


# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          8.
pairlistdist        13.5


# Integrator Parameters
timestep            2.0  ; # 2fs/step
rigidBonds          all ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10
margin              5

# Constant Temperature Control
langevin            on     ;# do langevin dynamics
langevinDamping     5      ;# damping coefficient (gamma) of 5/ps
langevinTemp        310
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens


# Periodic Boundary Conditions
cellBasisVector1      69.0               0.                        0.
cellBasisVector2      0.                76.                        0.
cellBasisVector3      0.                 0.                66.1230010986
cellOrigin           -0.0838125869632    0.121281333268    -0.300958424807

wrapAll             on


# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        70
PMEGridSizeY        80
PMEGridSizeZ        70


# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325  ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    310

# Output
outputName          $outputname

restartfreq         500      ;# 500steps = every 1ps
dcdfreq             250
xstFreq             250
outputEnergies      150
outputPressure      150

#############################################################
## EXTRA PARAMETERS                                        ##
#############################################################


#############################################################
## EXECUTION SCRIPT                                        ##
#############################################################

# Minimization
minimize            1000
reinitvels          310

run 500000 ;# 1000ps






-- 
-Rima

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Hi All,<br>I am trying to simulate a protein with a calcium ion and ligand attached using Amber forcefield in namd for 1ns, in two instances.<br>Case1: Simulating the protein with Calcium attached in 10A water box<br>Case2: Simulate the protein complex with inhibitor in a 10A water box
<br><br>In both the cases, right from frame 0, (I minimize for 1000 steps) the protein comes out of the water box and tethers to one edge, while the calcium ion and ligand comes out and tethers themselves to two other edges of the box. In other words they are partially immersed (just anchorched) to the water box on 3 different sides. Initially i thought it might be the parameters of Ca or ligand that is causing this, so I tried simulating the protein alone w/o Ca2+ even, it does the same thing, the protein comes out and even translates to another edge of the box after some 1000 frames randomly.
<br>The following is my .config file. Any guidance will be much appreciated.<br><br>amber&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; yes<br>parmfile&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; fxa_wat_ca.prmtop<br>ambercoor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; fxa_wat_ca.inpcrd<br><br><br><br>set temperature&nbsp;&nbsp;&nbsp;&nbsp; 310<br>set outputname&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; outFxa_ca&nbsp;&nbsp;&nbsp; 
<br><br>firsttimestep&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br><br><br>#############################################################<br>## SIMULATION PARAMETERS&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ##<br>#############################################################
<br><br># Input<br>paraTypeCharmm&nbsp;&nbsp;&nbsp; &nbsp; off<br>temperature&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>reassignFreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1000<br>reassignTemp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 25<br>reassignIncr&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 25<br>reassignHold&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 310<br><br><br># Force-Field Parameters<br>
exclude&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; scaled1-4<br>1-4scaling&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.0<br>cutoff&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 12.<br>switching&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on<br>switchdist&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.<br>pairlistdist&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.5<br><br><br># Integrator Parameters<br>timestep&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
2.0&nbsp; ; # 2fs/step<br>rigidBonds&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; all ;# needed for 2fs steps<br>nonbondedFreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>fullElectFrequency&nbsp; 2&nbsp; <br>stepspercycle&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10<br>margin&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5<br><br># Constant Temperature Control<br>langevin&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on&nbsp;&nbsp;&nbsp;&nbsp; ;# do langevin dynamics
<br>langevinDamping&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ;# damping coefficient (gamma) of 5/ps<br>langevinTemp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 310<br>langevinHydrogen&nbsp;&nbsp;&nbsp; off&nbsp;&nbsp;&nbsp; ;# don&#39;t couple langevin bath to hydrogens<br><br><br># Periodic Boundary Conditions<br>cellBasisVector1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
69.0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.<br>cellBasisVector2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 76.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.<br>cellBasisVector3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 66.1230010986&nbsp; <br>cellOrigin&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -
0.0838125869632&nbsp;&nbsp;&nbsp; 0.121281333268&nbsp;&nbsp;&nbsp; -0.300958424807<br><br>wrapAll&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on<br><br><br># PME (for full-system periodic electrostatics)<br>PME&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; yes<br>PMEGridSizeX&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 70<br>PMEGridSizeY&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 80<br>
PMEGridSizeZ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 70<br><br><br># Constant Pressure Control (variable volume)<br>useGroupPressure&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; yes ;# needed for rigidBonds<br>useFlexibleCell&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; no<br>useConstantArea&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; no<br><br>langevinPiston&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; on
<br>langevinPistonTarget&nbsp; 1.01325&nbsp; ;#&nbsp; in bar -&gt; 1 atm<br>langevinPistonPeriod&nbsp; 100.<br>langevinPistonDecay&nbsp;&nbsp; 50.<br>langevinPistonTemp&nbsp;&nbsp;&nbsp; 310<br><br># Output<br>outputName&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $outputname<br><br>restartfreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 500&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ;# 500steps = every 1ps
<br>dcdfreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 250<br>xstFreq&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 250<br>outputEnergies&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 150<br>outputPressure&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 150<br><br>#############################################################<br>## EXTRA PARAMETERS&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ##
<br>#############################################################<br><br><br>#############################################################<br>## EXECUTION SCRIPT&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ##<br>#############################################################
<br><br># Minimization<br>minimize&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1000<br>reinitvels&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 310<br>&nbsp; <br>run 500000 ;# 1000ps<br><br><br><br><br><br clear="all"><br>-- <br>-Rima

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From owner-namd-l@halifax.ks.uiuc.edu Mon Jan  8 14:33:15 2007
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Date: Mon, 08 Jan 2007 14:33:13 -0600
From: Peter Freddolino <petefred@ks.uiuc.edu>
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To: Rima Chaudhuri <rima.chaudhuri@gmail.com>
CC: namd-l@ks.uiuc.edu
Subject: Re: namd-l: Protein, ligand, ion out of the water box.
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Hi Rima,
have you tried visualizing this with the appropriate periodic boundary
conditions? It may be that your protein is in solvent, but doesn't
appear to be because its coordinates would not be wrapped unless the
whole chain crosses the boundary.
Peter

Rima Chaudhuri wrote:
> Hi All,
> I am trying to simulate a protein with a calcium ion and ligand
> attached using Amber forcefield in namd for 1ns, in two instances.
> Case1: Simulating the protein with Calcium attached in 10A water box
> Case2: Simulate the protein complex with inhibitor in a 10A water box
>
> In both the cases, right from frame 0, (I minimize for 1000 steps) the
> protein comes out of the water box and tethers to one edge, while the
> calcium ion and ligand comes out and tethers themselves to two other
> edges of the box. In other words they are partially immersed (just
> anchorched) to the water box on 3 different sides. Initially i thought
> it might be the parameters of Ca or ligand that is causing this, so I
> tried simulating the protein alone w/o Ca2+ even, it does the same
> thing, the protein comes out and even translates to another edge of
> the box after some 1000 frames randomly.
> The following is my .config file. Any guidance will be much appreciated.
>
> amber           yes
> parmfile        fxa_wat_ca.prmtop
> ambercoor       fxa_wat_ca.inpcrd
>
>
>
> set temperature     310
> set outputname      outFxa_ca   
>
> firsttimestep       0
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
> # Input
> paraTypeCharmm      off
> temperature             0
> reassignFreq         1000
> reassignTemp        25
> reassignIncr          25
> reassignHold        310
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.
> switching           on
> switchdist          8.
> pairlistdist        13.5
>
>
> # Integrator Parameters
> timestep            2.0  ; # 2fs/step
> rigidBonds          all ;# needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2 
> stepspercycle       10
> margin              5
>
> # Constant Temperature Control
> langevin            on     ;# do langevin dynamics
> langevinDamping     5      ;# damping coefficient (gamma) of 5/ps
> langevinTemp        310
> langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1      69.0               0.                        0.
> cellBasisVector2      0.                76.                        0.
> cellBasisVector3      0.                 0.                66.1230010986 
> cellOrigin           - 0.0838125869632    0.121281333268   
> -0.300958424807
>
> wrapAll             on
>
>
> # PME (for full-system periodic electrostatics)
> PME                 yes
> PMEGridSizeX        70
> PMEGridSizeY        80
> PMEGridSizeZ        70
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure      yes ;# needed for rigidBonds
> useFlexibleCell       no
> useConstantArea       no
>
> langevinPiston        on
> langevinPistonTarget  1.01325  ;#  in bar -> 1 atm
> langevinPistonPeriod  100.
> langevinPistonDecay   50.
> langevinPistonTemp    310
>
> # Output
> outputName          $outputname
>
> restartfreq         500      ;# 500steps = every 1ps
> dcdfreq             250
> xstFreq             250
> outputEnergies      150
> outputPressure      150
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
>
> # Minimization
> minimize            1000
> reinitvels          310
>  
> run 500000 ;# 1000ps
>
>
>
>
>
>
> -- 
> -Rima 

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Subject: namd-l: Anyone have catdcd-4.0 for BlueGene?
From: "Joshua D. Moore" <jdmoore@unity.ncsu.edu>
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Hi,

I was wondering if anyone has catdcd-4.0 compiled for BlueGene?  I use
BlueGene at SDSC.  I am not sure of the portability??  I would appreciate
any help, even in compiling.

Thanks.

Josh


--------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC  27695-7905
Phone: (919) 513-2051
Fax:   (919) 513-2470
Email:  jdmoore@unity.ncsu.edu
--------------------------------------------------

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Subject: namd-l: generalized born routine
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Is there a implicit solvation like generalized born routine in NAMD?=20

=20

=20

Regards,=20

=20

Rie Nygaard

Biochemist

7TM Pharma A/S

Fremtidsvej 3

DK-2970 H=F8rsholm

Denmark

=20

Phone:    +45 39 25 71 01

Fax:        +45 39 25 77 76

E-mail:    rn@7tm.com

Internet:  www.7tm.com =
<file:///C:\Documents%20and%20Settings\Aws\Application%20Data\Microsoft\S=
ignatures\www.7tm.com> =20


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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Is there a implicit solvation like generalized born =
routine
in NAMD? <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Regards, <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Rie Nygaard</span></font><o:p></o:p></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Biochemist<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>7TM Pharma A/S<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DDA =
style=3D'font-size:10.0pt;
font-family:Arial'>Fremtidsvej 3<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DDA =
style=3D'font-size:10.0pt;
font-family:Arial'>DK-2970 H=F8rsholm<o:p></o:p></span></font></p>

<p class=3DMsoNormal><u1:place u2:st=3D"on"><u1:country-region =
u2:st=3D"on"><font
size=3D2 face=3DArial><span lang=3DDA =
style=3D'font-size:10.0pt;font-family:Arial'>Denmark<o:p></o:p></span></f=
ont></u1:country-region></u1:place></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DDA =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DDA =
style=3D'font-size:10.0pt;
font-family:Arial'>Phone:&nbsp;&nbsp;&nbsp; +45 39 25 71 =
01</span></font><span
lang=3DDA><o:p></o:p></span></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +45 39 =
25 77
76<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>E-mail:&nbsp;&nbsp;&nbsp; <u><a =
href=3D"mailto:rn@7tm.com">rn@7tm.com</a><o:p></o:p></u></span></font></p=
>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Internet:&nbsp; <a
href=3D"file:///C:\Documents%20and%20Settings\Aws\Application%20Data\Micr=
osoft\Signatures\www.7tm.com"
title=3D"file:///C:/Documents%20and%20Settings/Aws/Application%20Data/Mic=
rosoft/Signatures/www.7tm.com">www.7tm.com</a>
<o:p></o:p></span></font></p>

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From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  9 11:29:25 2007
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Date: Tue, 9 Jan 2007 11:29:24 -0600
From: "Nitin Bhardwaj" <nbhardwaj@gmail.com>
To: vmd-l@ks.uiuc.edu, namd-l@ks.uiuc.edu
Subject: namd-l: Why does lipid move out of water box
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Dear VMD/NAMD users,

    I saw that during my simulation of a sigle lipid in a water box the
lipid moves out of the box. The water box seems to divide into 8 boxes. From
the mail archive I learnt that this is a problem of the VMD graphics and if
I added more periodic boxes, the lipid molecule would appear in the water
box.

I was just wondering why does this happen in the first place and what does
it mean. Does it mean that something is wrong with my system/parameters of
conf file? Also if I select "water within 10 of lipid", the water selected
is somewhere else in space and is no where near the lipid. Is it normal?

Thanks a lot in advance,
rgds,
Nitin

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<div>Dear VMD/NAMD users,</div>
<div>&nbsp;&nbsp;&nbsp; </div>
<div>&nbsp;&nbsp;&nbsp; I saw that during my simulation of a sigle lipid in a water box the lipid&nbsp;moves out of the box. The water box seems to divide into 8 boxes. From the mail archive I learnt that this is a problem of the VMD graphics and if I added more periodic boxes, the lipid molecule would appear in the water box. 
</div>
<div>&nbsp;</div>
<div>I was just wondering why does this happen in the first place and what does it mean. Does it mean that something is wrong with my system/parameters of conf file? Also if I select &quot;water within&nbsp;10 of lipid&quot;, the water selected is somewhere else in space and is no where near the lipid. Is it normal?
</div>
<div>&nbsp;</div>
<div>Thanks a lot in advance,</div>
<div>rgds,</div>
<div>Nitin<br clear="all"></div>

------=_Part_64245_1074456.1168363764609--

From owner-namd-l@halifax.ks.uiuc.edu Tue Jan  9 12:10:11 2007
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From: Simon Watson <simon.watson@ucl.ac.uk>
Subject: namd-l: Stray PME grid charges detected
Date: Tue, 9 Jan 2007 18:06:53 +0000
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Hi,

I have seen that several other people on this forum have been =20
affected by the same problem; I have followed all the threads, and =20
attempted all the suggestions but I am still suffering from the same =20
problem.

My system is composed of HIV protease, bound to saquinavir, in a =20
water box 81.93=C5 by 90.55=C5 by 81.80=C5.  The PME grid size was =20
originally 81 by 90 by 81 (x,y,z), and the protein and ligand are =20
restrained during the minimisation.  When I tried minimising, I =20
attained the following output:

ERROR: Stray PME grid charges detected: 0 sending to 7 for planes 18 19
ERROR: Stray PME grid charges detected: 0 sending to 6 for planes 16 17
ERROR: Stray PME grid charges detected: 0 sending to 23 for planes 63 =20=

64 65
ERROR: Stray PME grid charges detected: 0 sending to 22 for planes 60 =20=

61 62
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!
Warning: Stray PME grid charges ignored!
PRESSURE: 122 -1.47246e+07 1.52151e+06 -1.38893e+06 1.5201e+06 =20
-1.57702e+07 282057 -1.39157e+06 279814 -1.32042e+07
GPRESSURE: 122 -2.35315e+08 -1.20036e+07 1.84397e+07 -1.2128e+08 =20
5.7502e+06 -6.52172e+07 -5.55886e+07 6.14859e+06 -3.7112e+07
ENERGY:     122  99999999.9999    256946.1353      8404.9533         =20
0.0000       -1499602.7597   1171537.4338    492703.9185         =20
0.0000         0.0000       99999999.9999         0.0000  =20
99999999.9999  99999999.9999         0.0000      -14566345.2938 =20
-88892404.2323    606823.5931 -14566345.2938 -88892404.2323

I have attached my minimisation configuration file.  This is the =20
first time I have tried simulating with a ligand - all previous =20
simulations were apo-proteins.  For this reason I have had to set up =20
the system in AMBER, though I am simulating with NAMD.

As suggested, I tried increasing the cutoff from 12 to 14, 16, 18, =20
but this didn't help.  I also tried increasing the size of the PME =20
grid, ensuring it stayed a multiple of 2,3 and 5 in each direction, =20
but this also didn't help.

I found on the NAMDWiki Troubleshooting page that it could be because =20=

of an atom (probably hydrogen) moving to the other side of the cell, =20
making a bond extend across the cell.  I loaded up the .pdb and .crd =20
file in VMD and didn't see any very long bonds, except for 4 at the N-=20=

terminal amino acid that extend out very far out of the box, but =20
these are present even in different simulations that run with no =20
problems.  I also checked for uninitialised coordinates, but they all =20=

seemed okay.

I am not an experienced user of NAMD, and so was hoping that someone =20
could shed some light on any mistakes I have made or potential fixes =20
I have overlooked..

Thank you, in advance, for any help.

Simon.


--Apple-Mail-7--1067230582
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	name=eq0.conf
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	filename=eq0.conf

#input
paraTypeCharmm      off
amber yes
parmfile ../build/complex.top
readexclusions no
#unchanging information
# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5
# Integrator Parameters
timestep            2.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs steps
rigidtolerance      0.00001
rigidIterations     100
nonbondedFreq       1
fullElectFrequency  2
stepspercycle       10
wrapWater           on
wrapAll             on
#output
outputEnergies      50
outputPressure      50
################################################################################
#protocol specific information
cellBasisVector1	81.929  0.000  0.000
cellBasisVector2	 0.000 90.552  0.000
cellBasisVector3	 0.000  0.000 81.795
cellOrigin	 0.000  0.000  0.000
PME                 yes
PMEGridSizeX        81
PMEGridSizeY        90
PMEGridSizeZ        81
coordinates  ../build/complex.pdb
constraints  on
consexp  2
consref  ../build/complex.pdb ;#need all positions
conskfile  ../constraint/f4.pdb
conskcol  B
set temperature  50
temperature $temperature
binaryoutput  no
outputName  ../equilibration/eq0
minimize 2000

--Apple-Mail-7--1067230582--

From owner-namd-l@halifax.ks.uiuc.edu Wed Jan 10 10:08:50 2007
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Date: Wed, 10 Jan 2007 17:08:42 +0100
From: regafan@usc.es
To: namd-l@ks.uiuc.edu
Subject: namd-l: experimental phi-values as restraints
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Dear NAMD users,
I have to use experimental phi-values as restraints in a molecular  
dynamics simulation to determine a ensemble of structures representing  
the transition state of a protein folding, and I don´t know how to  
start. Has anybody done something related to that? Does anybody know  
where could I find a tutorial of this subject?
Any help would be wellcome!
Thanks a lot in advance. Best wishes,

Rebeca García
Post-doctoral student
Parc Cientifi Barcelona
Spain
regafan@usc.es


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 04:24:06 2007
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Date: Thu, 11 Jan 2007 15:54:04 +0530
From: "amit dong" <amitdong@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: H-bond energy
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Hi,
I need to calculate H-bond energy between two pair of atoms for a whole
trajectory. I was wondering if there is any quick way of doing it.
Thanks
Amit

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<div>Hi,</div>
<div>I need to calculate H-bond energy between two pair of atoms for a whole trajectory. I was wondering if there is any quick way of doing it.</div>
<div>Thanks</div>
<div>Amit</div>

------=_Part_10902_5842696.1168511044554--

From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 08:39:34 2007
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Date: Thu, 11 Jan 2007 09:39:32 -0500
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From: Kramer Campen <campen@geosc.psu.edu>
Subject: namd-l: Replica Exchange MD using Amber parameters
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Hey Folks:

I'd like to run some replica exchange simulations in NAMD using AMBER 
parameters.  Does anyone have any experience doing this?  Could anyone give 
me any insight into what I'd to alter in order to make this happen?

Thanks in advance for any insight.

Kramer


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 15:48:05 2007
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From: Jon Halverson <jhalvers@che.ccny.cuny.edu>
Subject: namd-l: "CWeb performance data sent to wrong processor..."
Date: Thu, 11 Jan 2007 16:47:57 -0500
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A job aborted on DataStar at SDSC with the following error message:

------------- Processor 3 Exiting: Called CmiAbort ------------
Reason: CWeb performance data sent to wrong processor...

------------- Processor 83 Exiting: Called CmiAbort ------------
Reason: CWeb performance data sent to wrong processor...

------------- Processor 89 Exiting: Called CmiAbort ------------
Reason: CWeb performance data sent to wrong processor...

------------- Processor 5 Exiting: Called CmiAbort ------------
Reason: CWeb performance data sent to wrong processor...

------------- Processor 29 Exiting: Called CmiAbort ------------
Reason: CWeb performance data sent to wrong processor...

etc.

Why did this happen and how do I prevent it from happening again?


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 16:15:59 2007
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Date: Fri, 12 Jan 2007 09:15:54 +1100 (EST)
Subject: Re: namd-l: Replica Exchange MD using Amber parameters
From: "Mark Abraham" <mark.abraham@anu.edu.au>
To: namd-l@ks.uiuc.edu
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> Hey Folks:
>
> I'd like to run some replica exchange simulations in NAMD using AMBER
> parameters.  Does anyone have any experience doing this?  Could anyone
> give
> me any insight into what I'd to alter in order to make this happen?

You'd need the AMBER parameters expressed in CHARMM format, and thereafter
probably everything else will be the same.

Mark


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 17:14:47 2007
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Subject: Re: namd-l: Replica Exchange MD using Amber parameters
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Hey Mark:

I've been experimenting with this a bit and it appears that your statement 
isn't true.  That is, you can run your replica exchange simulation using 
the usual "amber yes" and "parmfile xxx.top" commands.  The existing 
scripts to display the results require a psf file so this would require 
additional modification but as far as actually generating the data it 
appears that you can use Amber parameters in Amber format easily.

Kramer



At 09:15 AM 1/12/2007 +1100, Mark Abraham wrote:
> > Hey Folks:
> >
> > I'd like to run some replica exchange simulations in NAMD using AMBER
> > parameters.  Does anyone have any experience doing this?  Could anyone
> > give
> > me any insight into what I'd to alter in order to make this happen?
>
>You'd need the AMBER parameters expressed in CHARMM format, and thereafter
>probably everything else will be the same.
>
>Mark


From owner-namd-l@halifax.ks.uiuc.edu Thu Jan 11 19:37:37 2007
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Date: Thu, 11 Jan 2007 19:37:34 -0600
From: "Alexander Vaughn" <aevaughn@gmail.com>
To: namd-l@ks.uiuc.edu
Subject: namd-l: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
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This is the outpute of trying to run a namd2 minimization calculation from 3
different pdb files(one protein, one water, and one the residue), and using
one topology file that has information for all three parts.  The psfgen
program ran without any errors, the namd2 program however does have a fatal
error as seen below.
Thanks in advance for your assistance!

Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info:
....
Info: 1 NAMD  2.6  Linux-i686  1    ubuntumachine  aevaughn
Info: Running on 1 processors.
Info: 7244 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is 2LBD.conf
TCL: Suspending until startup complete.
...
Info: COORDINATE PDB         ./2LBDpro.pdb ./2LBDwat.pdb ./2LBDret.pdb
Info: STRUCTURE FILE         ./2LBD.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             ./top_retacid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp
LINE=*MASS     1 H      1.00800 H ! polar H*
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
./top_retacid.inp
LINE=*MASS     1 H      1.00800 H ! polar H*

Stack Traceback:
....
Charm++ fatal error:
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp
LINE=*MASS     1 H      1.00800 H ! polar H*

-- 
Alex Vaughn
aevaughn@uab.edu

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This is the outpute of trying to run a namd2 minimization calculation from 3 different pdb files(one protein, one water, and one the residue), and using one topology file that has information for all three parts.&nbsp; The psfgen program ran without any errors, the namd2 program however does have a fatal error as seen below.
<br>Thanks in advance for your assistance!<br><br>Charm++: standalone mode (not using charmrun)<br>Info: NAMD 2.6 for Linux-i686<br>Info: <br>Info: Please visit <a href="http://www.ks.uiuc.edu/Research/namd/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.ks.uiuc.edu/Research/namd/
</a><br>Info: and send feedback or bug reports to <a href="mailto:namd@ks.uiuc.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">namd@ks.uiuc.edu</a><br>Info: <br>....<br>Info: 1 NAMD&nbsp; 2.6&nbsp; Linux-i686&nbsp; 1&nbsp;&nbsp;&nbsp; ubuntumachine&nbsp; aevaughn
<br>Info: Running on 1 processors.<br>
Info: 7244 kB of memory in use.<br>Info: Memory usage based on mallinfo<br>Info: Configuration file is 2LBD.conf<br>TCL: Suspending until startup complete.<br>...<br>Info: COORDINATE PDB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ./2LBDpro.pdb ./2LBDwat.pdb ./2LBDret.pdb
<br>Info: STRUCTURE FILE&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ./2LBD.psf<br>Info: PARAMETER file: CHARMM format! <br>Info: PARAMETERS&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ./top_retacid.inp<br>Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS<br>FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp
<br>LINE=*MASS&nbsp;&nbsp;&nbsp;&nbsp; 1 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.00800 H ! polar H*<br>------------- Processor 0 Exiting: Called CmiAbort ------------<br>Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp<br>LINE=*MASS&nbsp;&nbsp;&nbsp;&nbsp; 1 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
1.00800 H ! polar H*<br><br>Stack Traceback:<br>....<br>Charm++ fatal error:<br>FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp<br>LINE=*MASS&nbsp;&nbsp;&nbsp;&nbsp; 1 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.00800 H ! polar H*<br><br>-- <br>Alex Vaughn
<br><a href="mailto:aevaughn@uab.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">aevaughn@uab.edu</a>


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Subject: Re: namd-l: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
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A parameter file is separate from the topology file (the NAMD  
tutorial has pretty good descriptions of both at the end).  In your  
namd input file, you will need to source the correct parameter file;  
probably the standard charmm par_all27_prot_lipid.inp will work.


On Jan 11, 2007, at 7:37 PM, Alexander Vaughn wrote:

> This is the outpute of trying to run a namd2 minimization  
> calculation from 3 different pdb files(one protein, one water, and  
> one the residue), and using one topology file that has information  
> for all three parts.  The psfgen program ran without any errors,  
> the namd2 program however does have a fatal error as seen below.
> Thanks in advance for your assistance!
>
> Charm++: standalone mode (not using charmrun)
> Info: NAMD 2.6 for Linux-i686
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd@ks.uiuc.edu
> Info:
> ....
> Info: 1 NAMD  2.6  Linux-i686  1    ubuntumachine  aevaughn
> Info: Running on 1 processors.
> Info: 7244 kB of memory in use.
> Info: Memory usage based on mallinfo
> Info: Configuration file is 2LBD.conf
> TCL: Suspending until startup complete.
> ...
> Info: COORDINATE PDB         ./2LBDpro.pdb ./2LBDwat.pdb ./2LBDret.pdb
> Info: STRUCTURE FILE         ./2LBD.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS             ./top_retacid.inp
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./ 
> top_retacid.inp
> LINE=*MASS     1 H      1.00800 H ! polar H*
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./ 
> top_retacid.inp
> LINE=*MASS     1 H      1.00800 H ! polar H*
>
> Stack Traceback:
> ....
> Charm++ fatal error:
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./ 
> top_retacid.inp
> LINE=*MASS     1 H      1.00800 H ! polar H*
>
> -- 
> Alex Vaughn
> aevaughn@uab.edu


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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; ">A parameter file is separate =
from the topology file (the NAMD tutorial has pretty good descriptions =
of both at the end).=A0 In your namd input file, you will need to source =
the correct parameter file; probably the standard charmm =
par_all27_prot_lipid.inp will work.<DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV><DIV><DIV>On Jan 11, 2007, =
at 7:37 PM, Alexander Vaughn wrote:</DIV><BR =
class=3D"Apple-interchange-newline"><BLOCKQUOTE type=3D"cite">This is =
the outpute of trying to run a namd2 minimization calculation from 3 =
different pdb files(one protein, one water, and one the residue), and =
using one topology file that has information for all three parts.=A0 The =
psfgen program ran without any errors, the namd2 program however does =
have a fatal error as seen below. <BR>Thanks in advance for your =
assistance!<BR><BR>Charm++: standalone mode (not using =
charmrun)<BR>Info: NAMD 2.6 for Linux-i686<BR>Info: <BR>Info: Please =
visit <A href=3D"http://www.ks.uiuc.edu/Research/namd/" target=3D"_blank" =
onclick=3D"return top.js.OpenExtLink(window,event,this)"> =
http://www.ks.uiuc.edu/Research/namd/ </A><BR>Info: and send feedback or =
bug reports to <A href=3D"mailto:namd@ks.uiuc.edu" target=3D"_blank" =
onclick=3D"return =
top.js.OpenExtLink(window,event,this)">namd@ks.uiuc.edu</A><BR>Info: =
<BR>....<BR>Info: 1 NAMD=A0 2.6=A0 Linux-i686=A0 1=A0=A0=A0 =
ubuntumachine=A0 aevaughn <BR>Info: Running on 1 processors.<BR> Info: =
7244 kB of memory in use.<BR>Info: Memory usage based on =
mallinfo<BR>Info: Configuration file is 2LBD.conf<BR>TCL: Suspending =
until startup complete.<BR>...<BR>Info: COORDINATE PDB=A0=A0=A0=A0=A0=A0=A0=
=A0 ./2LBDpro.pdb ./2LBDwat.pdb ./2LBDret.pdb <BR>Info: STRUCTURE =
FILE=A0=A0=A0=A0=A0=A0=A0=A0 ./2LBD.psf<BR>Info: PARAMETER file: CHARMM =
format! <BR>Info: PARAMETERS=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =
./top_retacid.inp<BR>Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA =
PARAMETERS<BR>FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE =
./top_retacid.inp <BR>LINE=3D*MASS=A0=A0=A0=A0 1 H=A0=A0=A0=A0=A0 =
1.00800 H ! polar H*<BR>------------- Processor 0 Exiting: Called =
CmiAbort ------------<BR>Reason: FATAL ERROR: UNKNOWN PARAMETER IN =
CHARMM PARAMETER FILE ./top_retacid.inp<BR>LINE=3D*MASS=A0=A0=A0=A0 1 =
H=A0=A0=A0=A0=A0 1.00800 H ! polar H*<BR><BR>Stack =
Traceback:<BR>....<BR>Charm++ fatal error:<BR>FATAL ERROR: UNKNOWN =
PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp<BR>LINE=3D*MASS=A0=A0=
=A0=A0 1 H=A0=A0=A0=A0=A0 1.00800 H ! polar H*<BR><BR>-- <BR>Alex Vaughn =
<BR><A href=3D"mailto:aevaughn@uab.edu" target=3D"_blank" =
onclick=3D"return =
top.js.OpenExtLink(window,event,this)">aevaughn@uab.edu</A></BLOCKQUOTE></=
DIV><BR></DIV></BODY></HTML>=

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<font size="+1"><font face="Nimbus Roman No9 L"></font></font>To NAMD
Developers and Users,<br>
<br>
I have a problem getting NAMD2.6 working in parallel. The efficiency is
getting worse when I use&nbsp; more than 4 cpus per node.<br>
<br>
Can any one check the way I installed the NAMD on my system?<br>
And if it is OK, I appreciate any suggestions to solve this problem.<br>
<br>
<br>
<font color="#ff0000">My System:</font><br>
<b>Dell 1955 Linux cluster. Each node is equipped with two Quad-core
Intel Xeon EM64T processors (2.6GHz) and 8 GB of memory. <span
 class="qa_a">All nodes are connected with Gigabit Ethernet</span>. </b><span
 class="qa_a"><b>The cluster's EM64T processors run a 64-bit Linux
kernel.</b><br>
<br>
<br>
<font color="#ff0000">Installation Instructions:<br>
<br>
<b><font color="#000000"><font color="#3333ff">fftw-2.1.5 Installation:</font><br>
-------------------------<br>
<br>
./configure --prefix=/ibrix/home/mfm42/opt/fftw --enable-mpi
--enable-float --enable-type-prefix --enable-debug
--enable-dependency-tracking --enable-static<br>
<br>
make<br>
<br>
make install<br>
<br>
###################################################################################<br>
<font color="#3333ff"><br>
t</font><font color="#3333ff">cl-8.4.13 Installation:</font><br>
------------------------<br>
<br>
./configure --prefix=/ibrix/home/mfm42/opt/tcl --enable-64bit
--disable-shared<br>
<br>
make<br>
<br>
make install<br>
<br>
###################################################################################<br>
<br>
<font color="#3333ff">charm++ Installation:</font><br>
---------------------<br>
<br>
Edit the file charm/src/arch/mpi-linux-amd64/conv-mach.sh:<br>
1)change mpiCC to mpicxx<br>
2)use /opt/mpich/gnu/bin as the path to mpicc and mpicxx.<br>
<br>
./build charm++ mpi-linux-amd64 --basedir=/opt/mpich/gnu
--no-build-shared -O -verbose -DCMK_OPTIMIZE=1 &gt; build.log<br>
<br>
###################################################################################<br>
<br>
<font color="#3333ff">namd Installation:</font><br>
------------------<br>
<br>
Edit namd/Make.charm<br>
(set CHARMBASE to the full path to charm-??)<br>
<br>
Edit various configuration files:<br>
1) namd/arch/Linux-amd64.fftw&nbsp;&nbsp;&nbsp; (fix path to files,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; delete -I$(HOME)/fftw/include and
-L$(HOME)/fftw/lib)<br>
2) namd/arch/Linux-amd64.tcl&nbsp;&nbsp;&nbsp;&nbsp; (fix path to files<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; delete -I$(HOME)/tcl/include and
-L$(HOME)/tcl/lib<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; use -ltcl8.4 instead of -ltcl8.3<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; add -DUSE_NON_CONST to TCLFLAGS)<br>
3) namd/arch/Linux-amd64-MPI.arch use /opt/mpich/gnu/bin as a path to<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; mpicxx and mpicc instead of g++/gcc<br>
<br>
Set up build directory and compile:<br>
&nbsp; ./config tcl fftw Linux-amd64-MPI<br>
&nbsp; cd Linux-amd64-MPI<br>
&nbsp; make &gt; make.log</font></b><br>
</font><br>
<br>
<br>
</span><b><font color="#ff0000">Submission command: </font></b><br>
<b>/opt/mpiexec/bin/mpiexec
/ibrix/home/mfm42/opt/namd-GE/Linux-amd64-MPI/namd2 gamma_150_sys.namd
"+strategy USE_GRID" &gt; gamma_150_sys.log</b><br>
<br>
<br>
Thanks<br>
<br>
Morad Alawneh<br>
Department of Chemistry and Biochemistry, BYU<br>
Provo, UT<br>
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Date: Sat, 13 Jan 2007 09:18:46 -0700
From: Morad Alawneh <alawneh@chem.byu.edu>
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To: Brian Bennion <bennion1@llnl.gov>, namd-l <namd-l@ks.uiuc.edu>
Subject: Re: namd-l: Scalability problem with NAMD2.6 on Intel Xeon   EM64T
 processors
References: <45A7BDA7.9010409@chem.byu.edu> <7.0.0.16.2.20070112102819.022bc3f8@llnl.gov>
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<font size="+1"><font face="Nimbus Roman No9 L"><br>
Thank you for answering my inquiry.<br>
My system size is 12,458 atoms, and the scalability is fine when I use
the infiniband of this linux cluster.<br>
<br>
After a lot of debugging, I think you are right, it is a hardware
problem.<br>
<br>
Here is the time information for each number of cpus:<br>
<br>
Info: Benchmark time: 4 CPUs 0.206016 s/step 1.19222 days/ns 32100 kB
memory<br>
TIMING: 600&nbsp; CPU: 129.219, 0.206016/step&nbsp; Wall: 129.219, 0.206016/step,
572.231 hours remaining, 32100 kB of memory in use.<br>
<br>
Info: Benchmark time: 8 CPUs 0.149766 s/step 0.866699 days/ns 23608 kB
memory<br>
TIMING: 600&nbsp; CPU: 96.7031, 0.149766/step&nbsp; Wall: 96.7031, 0.149766/step,
415.991 hours remaining, 23608 kB of memory in use.<br>
<br>
Info: Benchmark time: 16 CPUs 0.114141 s/step 0.660536 days/ns 16032 kB
memory<br>
TIMING: 600&nbsp; CPU: 79.2344, 0.11418/step&nbsp; Wall: 79.2344, 0.11418/step,
317.147 hours remaining, 16032 kB of memory in use.<br>
<br>
<br>
Thanks.<br>
<br>
Morad Alawneh<br>
<br>
</font></font><br>
Brian Bennion wrote:
<blockquote cite="mid7.0.0.16.2.20070112102819.022bc3f8@llnl.gov"
 type="cite">Hello Morad,<br>
  <br>
How big is the system your are studying?&nbsp; Perhaps it does not have
enough atoms to justify more that 4 cpus.<br>
The switch/cables may be defective. <br>
I am not sure that adding debugging symbols and dependency tracking to
the fftw libraries is a good idea for production simulations.<br>
The compile wiki at <a
 href="http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile"
 eudora="autourl">http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile</a><br>
Doesn't have these flags for ffttw compilation.<br>
  <br>
Can you post some timing information to so how bad it really is?<br>
Regards<br>
Brian Bennion<br>
  <br>
At 08:56 AM 1/12/2007, you wrote:<br>
  <blockquote type="cite" class="cite" cite="">To NAMD Developers and
Users,<br>
    <br>
I have a problem getting NAMD2.6 working in parallel. The efficiency is
getting worse when I use&nbsp; more than 4 cpus per node.<br>
    <br>
Can any one check the way I installed the NAMD on my system?<br>
And if it is OK, I appreciate any suggestions to solve this
problem.<br>
    <br>
    <br>
    <font color="#ff0000">My System:</font><br>
    <b>Dell 1955 Linux cluster. Each node is equipped with two
Quad-core
Intel Xeon EM64T processors (2.6GHz) and 8 GB of memory. All nodes are
connected with Gigabit Ethernet. The cluster's EM64T processors run a
64-bit Linux kernel.</b><br>
    <br>
    <br>
    <font color="#ff0000">Installation Instructions:<br>
    <br>
    </font><font color="#3333ff"><b>fftw-2.1.5 Installation:</b></font><b><br>
-------------------------<br>
    <br>
./configure --prefix=/ibrix/home/mfm42/opt/fftw --enable-mpi
--enable-float --enable-type-prefix --enable-debug
--enable-dependency-tracking --enable-static<br>
    <br>
make<br>
    <br>
make install<br>
    <br>
###################################################################################<br>
    <font color="#3333ff"><br>
tcl-8.4.13 Installation:</font><br>
------------------------<br>
    <br>
./configure --prefix=/ibrix/home/mfm42/opt/tcl --enable-64bit
--disable-shared<br>
    <br>
make<br>
    <br>
make install<br>
    <br>
###################################################################################<br>
    <br>
    <font color="#3333ff">charm++ Installation:</font><br>
---------------------<br>
    <br>
Edit the file charm/src/arch/mpi-linux-amd64/conv-mach.sh:<br>
1)change mpiCC to mpicxx<br>
2)use /opt/mpich/gnu/bin as the path to mpicc and mpicxx.<br>
    <br>
./build charm++ mpi-linux-amd64 --basedir=/opt/mpich/gnu
--no-build-shared -O -verbose -DCMK_OPTIMIZE=1 &gt; build.log<br>
    <br>
###################################################################################<br>
    <br>
    <font color="#3333ff">namd Installation:</font><br>
------------------<br>
    <br>
Edit namd/Make.charm<br>
(set CHARMBASE to the full path to charm-??)<br>
    <br>
Edit various configuration files:<br>
1) namd/arch/Linux-amd64.fftw&nbsp;&nbsp;&nbsp; (fix path to files,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
delete -I$(HOME)/fftw/include and -L$(HOME)/fftw/lib)<br>
2) namd/arch/Linux-amd64.tcl&nbsp;&nbsp;&nbsp;&nbsp; (fix path to
files<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
delete -I$(HOME)/tcl/include and -L$(HOME)/tcl/lib<br>
&nbsp;&nbsp;&nbsp;&nbsp