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Am 05.10.2012 12:39, schrieb gmx-users-requ...@gromacs.org:
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Today's Topics:
1. Re: regarding g_covar (ran friedman)
2. Re: The No. of the CO2 melecules in top file can not be
updated correctly (Justin Lemkul)
3. Re: PME error for energy minimization of TMD in lipid bilayer
(Justin Lemkul)
4. Re: Error There is no domain decomposition for 6 nodes that
is compatible (Justin Lemkul)
5. Re: Interaction energy calculation.. (Justin Lemkul)
6. Re: Interaction energy calculation.. (rama david)
7. Re: Interaction energy calculation.. (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Fri, 5 Oct 2012 12:01:31 +0200
From: ran friedman<ran.fried...@gmail.com>
Subject: Re: [gmx-users] regarding g_covar
To: gmx-users@gromacs.org
Message-ID:
<cad++iooghk3pe5w6w2ezbwadch8inrozn6xnd6+hakrnipm...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Did you try using another structural form (gro or pdb) instead of tpr?
The most recent version that I have is for GMX 4.04. I'll send it to you
off list.
Ran
Message: 6
Date: Fri, 5 Oct 2012 11:30:41 +0300
From: "R.Vidya Rajendran (10PHD013)"<vidya2...@vit.ac.in>
Subject: [gmx-users] regarding g_covar
To: gmx-users@gromacs.org
Message-ID:
<CAGqYpqAhDbCmCv=xreoa-7y0buy5odck6aaa_b5qlr7rjw+...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hello Everybody,
I am using g_covar with -xpmc flag in-oder to generate matrix of
atomic correlation coefficients. At present I am using g_covar script
given by Ran, which I downloaded from gromacs user modified script
pool.
Since Ran's script is for gromacs 3.3.3 and it not accept .trp input
from upgraded version (eg 4.5.5).
Anybody have upgraded g_covar which can do the same job.
regards
Vidya
------------------------------
Message: 2
Date: Fri, 05 Oct 2012 06:05:31 -0400
From: Justin Lemkul<jalem...@vt.edu>
Subject: Re: [gmx-users] The No. of the CO2 melecules in top file can
not be updated correctly
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<506eb0eb.8010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/5/12 5:18 AM, Bao Kai wrote:
Hi, Justin,
Thank you for your reply.
It is a little weird and inconvienient that genbox does not update the No.
of solute molecules. Is it designed in this way? Does it have any reason
for that?
The principal function of genbox is to solvate systems, usually with water. The
other things it can do are added on, but the code is designed around the most
commmon usage. Insertion of molecules is not guaranteed to work, so if a user
specifies a number of molecules to add and then genbox cannot, then either it
will update with topology with the actual number inserted (which may disagree
with the command line, and users may ignore any failures and proceed) or the
number requested (which may then fail for the opposite reason). You can see how
it becomes a slippery slope to try to make software out-think the user.
For my case, the inear, 3-atom model of CO2 works pretty well. I got the
model from a paper from Zhenhao Duan. I guess I will use this model for
the project before I get something wrong.
Good luck. Linear angles are generally not stable.
-Justin
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