[gmx-users] comm_grps

[priyanka srivastava]

Dear Jochen,

Many thanx for your reply. It is really very nice to hear that it shouldn't make any big difference since I have already completed several lipid peptide simulations for ~20ns. :-)

thanks and regards,
Pri...

----- Original Message ----
From: Jochen Hub <jhub at gwdg.de>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, 24 January, 2008 5:27:49 PM
Subject: Re: [gmx-users] comm_grps

In case of a lipid membrane simulation I would consider it as more 
natural to keep the membrane in the center of the box, hence to apply 
the com correction to the lipids only. In the end it might, however,
 not 
make a big difference...

Jochen

priyanka srivastava wrote:
> Dear All,
>
> I am a little confused with the application of
> comm_grps. I have a lipid-peptide system in which I am
> using the default values i.e. 
>
> comm_mode: linear
> nstcomm: 1
> comm_grps: whole system
>
> Is there something wrong with defining comm_grps =
> whole system for the lipid-peptide case? Is it
> necessary to define lipid+peptide and solvent
> separately?
>
> Eagerly waiting for the reply,
> Priyanka
>
>
>
>      
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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************ 

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