[gmx-users] simulation of a peptide anchored to a support
Mark.Abraham at anu.edu.au
Thu May 19 11:17:20 CEST 2011
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
> 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.
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