Fw: [gmx-users] make an index file of COM of lipid bilayer

[Shima Arasteh]

Thanks for your reply.
But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or .... know for it?





Sincerely,
Shima

----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, July 16, 2013 3:39 PM
Subject: Re: [gmx-users] make an index file of COM of lipid bilayer




On 7/16/13 5:30 AM, Shima Arasteh wrote:
>
>
> Hi,
>
>
> Would you please let me know how can I make an index file of COM of lipid membrane?
> I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point?
>
> I want to include this index file as the ref_group in Umbrella Sampling.
>

Index files can't specify positions, only atoms.  In this case, you don't even 
need a special index group - just use the membrane.  The pull code uses the COM 
of the selected group, so if you specify your membrane, mdrun knows to use its COM.

-Justin

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