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

[Mark Abraham]

On 19/05/2011 8:10 PM, Anna Marabotti wrote:
> 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).

If the box is periodic, then there is no wall to it. If the box is not 
periodic, then you have bigger problems to solve.

It sounds to me like you're trying to model something that is not 
reality. The peptide "fixed on a rigid support" still interacts with the 
support and the solvent (e.g. the support generates ordered solvent, 
which affects the peptide), and any attempt to artificially reduce the 
degrees of freedom of the simulation runs the risk that you have 
constructed your observations in advance through choosing your initial 
conditions.

Mark

> 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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