VMD-L Mailing List

From: Shahid Qamar (qamar13_at_hotmail.com)
Date: Fri Apr 15 2005 - 13:19:24 CDT

I have the same problem but otherway round. I see good structure on Linux
but messed up structure on windows but when I look the minimised structure
on both machines it looks perfact. You might wanna look at the minimised
structure.

Thanks

From: Hyonseok Hwang <danggi_at_northwestern.edu>
To: John Stone <johns_at_ks.uiuc.edu>
CC: VMD <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: wrong bond and bond breaking
Date: Fri, 15 Apr 2005 12:24:00 -0500
MIME-Version: 1.0
Received: from halifax.ks.uiuc.edu ([130.126.120.36]) by mc2-f30.hotmail.com
with Microsoft SMTPSVC(6.0.3790.211); Fri, 15 Apr 2005 11:03:24 -0700
Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36])by
halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id
j3FHOAVf007900(version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256
verify=NOT)for <vmd-l-outgoing_at_halifax.ks.uiuc.edu>; Fri, 15 Apr 2005
12:24:10 -0500 (CDT)
Received: (from majordom_at_localhost)by halifax.ks.uiuc.edu
(8.12.10/8.12.9/Submit) id j3FHOAOf007899for vmd-l-outgoing; Fri, 15 Apr
2005 12:24:10 -0500 (CDT)
Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu
[129.105.16.54])by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id
j3FHO8Ve007881;Fri, 15 Apr 2005 12:24:08 -0500 (CDT)
Received: (from mailnull_at_localhost)by lulu.it.northwestern.edu
(8.12.10/8.12.10) id j3FHO7YZ021586;Fri, 15 Apr 2005 12:24:07 -0500 (CDT)
Received: from [127.0.0.1] (tcg055206.theory.northwestern.edu
[129.105.55.206]) by lulu.it.northwestern.edu via smap (V2.0)id xma021432;
Fri, 15 Apr 05 12:24:02 -0500
X-Message-Info: KtxBqYfPyq2O9LeBPrDNalCefDdh1Q8Gmt7TLfE6tzE=
X-Authentication-Warning: halifax.ks.uiuc.edu: majordom set sender to
owner-vmd-l_at_ks.uiuc.edu using -f
User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103)
X-Accept-Language: en-us, en
References: <425FE873.9040005_at_northwestern.edu>
<20050415164608.GD19970_at_moline.ks.uiuc.edu>
Precedence: bulk
Return-Path: owner-vmd-l_at_halifax.ks.uiuc.edu
X-OriginalArrivalTime: 15 Apr 2005 18:03:24.0899 (UTC)
FILETIME=[6B08EB30:01C541E5]

So sorry for my insufficient information and thank you for your reply, John.

Those two VMDs are installed in separate machines. One VMD(ver 1.8.3) is
installed in a linux box and the other one (ver 1.8.2) is installed in my
windows laptop. I had had this problem in the VMD 1.8.2 in the linux machine
and I insatlled the 1.8.3 version in the linux, but I still have the
problem.

The similar probmem happens when I visualize the many water molecules (there
are only water molecules in the system) in the linux machine(ver 1.8.2). If
I visualize a small number of water molecules, then that's fine, but when I
try to show the whole number of water molecules (around 1500 water
molecules), wrong bonds beween an oxygen in one water and hydrogens in
another water are made and the picture is messed up. Interestingly, this
problem does not appear in the windows version (1.8.2)of VMD.

The information of linux I'm using is :
Linux version 2.4.22-1.2188.nptlsmp (bhcompile_at_daffy.perf.redhat.com) (g
         cc version 3.2.3 20030422 (Red Hat Linux 3.2.3-6)) #1 SMP INTEL
Xeon dual processor 2.80GHz.

Thanks again.

-Hyon

John Stone wrote:
>Hi,
> Are you running both versions of VMD on the same machine (dual boot)?
>Or are these on different machines? What version of Linux are you running
>VMD on, and which version of VMD are you asking about. The more
>information,
>the easier it will be for us to help solve your problem.
>
>Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Fri, Apr 15, 2005 at 11:14:43AM -0500, Hyonseok Hwang wrote:
>
>>Dear all,
>>
>>Sometimes the linux version of VMD shows wrong bonds and wrong bond
>>breaking of a molecule and messes up the molecule finally. But the windows
>>version of VMD shows the same molecule correctly. What's wrong with my
>>linux version of VMD. Do I have to install something?
>>Thanks a lot in advance!
>>
>>-Hyon
>
>