[gmx-users] Stretching a single peptide for PMF calculation

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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