[gmx-users] Stretching a single peptide for PMF calculation
feenstra at chem.vu.nl
Mon Aug 30 08:29:36 CEST 2004
Sekwan Oh wrote:
> Dear gmx-users,
> I would like to calculate PMF by stretching a single polypeptide
> molecule in water for free energy analysis.
> My idea is to put position-restraint on one atom in one end of the
> polypeptide and pull the atom in the other end to a certain axis.
> However, I couldn't find relevant examples on the manual.
> Is this idea reasonable for Gromacs?
Yes - you'd need the 'pull' code. Look for it in the manual, and in this list.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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