R: Re: [gmx-users] simulation of a peptide anchored to a support

[Anna Marabotti]

Dear Mark,
thank you for suggestions. I suspected that freezegrps does not work with
NPT but I'm not sure that position restraints work with the same final
effect.
Concerning fixing the peptide on the simulation box, I would like to
simulate as much as possible the fact that the peptide is fixed on a rigid
support, so I'd like to avoid a peptide that rotates and fluctuates into the
simulation box. I wonder if there is a way to fix the peptide like a handle
in one of the walls of the box itself (obviously, in the internal part of
the box).
Thanks a lot to anybody will contribute to the discussion!
Anna

Date: Thu, 19 May 2011 19:17:20 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] simulation of a peptide anchored to a support
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DD4E020.2080403 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 19/05/2011 7:09 PM, Anna Marabotti wrote:
> Dear gmx-users,
> I would like to simulate the conformational behaviour of a peptide 
> covalently anchored to a rigid support with its N- and C-ter. I'm not 
> interested in simulating the support, so I wonder if there is a way to 
> simulate the peptide with its N- and C-ter fixed. Could freezegrps 
> work for this?

Probably - but not with NPT. However, a strong position restraint is 
probably easier.

> Otherwise (or in addition) could I fix the peptide on one side of the 
> simulation box, in order to avoid the fluctuation of the peptide into 
> the solvent?

Not sure what you mean.

> Finally, do I have to add special constraints/restraints to my molecule?

Depends on the strategy.

Mark
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