[gmx-users] help

[Marlon Hinner]

Please unsubscribe. Thank you.

Best,

Marlon

Am 05.10.2012 12:39, schrieb gmx-users-request at gromacs.org:
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> Today's Topics:
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>     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.friedman at gmail.com>
> Subject: Re: [gmx-users] regarding g_covar
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAD++iooGhK3pe5W6W2EZbWADCH8iNRoZn6XnD6+HaKRnipmKvw at 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)"<vidya2010 at vit.ac.in>
> Subject: [gmx-users] regarding g_covar
> To: gmx-users at gromacs.org
> Message-ID:
>          <CAGqYpqAhDbCmCv=XreOA-7Y0BUy5oDCK6aAa_b5qLR7RjW+PAg at 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<jalemkul at 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 at gromacs.org>
> Message-ID:<506EB0EB.8010301 at 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
>