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

[Mark Abraham]

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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