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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