AMBER Archive (2005)

Subject: AMBER: Free energy extimate for the same structure but different conformers

From: claudio (claudio_at_photo.chem.uottawa.ca)
Date: Mon Feb 21 2005 - 14:56:10 CST

Dear All,

I'd like to monitor the change in the free energy in function of time of
a system containing about 1000 atoms in an explicit solvent with about
4000 TIP3P water molecules. There were no particular problems in the
equilibration which went nicely up to 2ns. However, it might be
interesting to plot along the same trajectory the change of free energy.

All the cases mentioned in Amber imply a change of the structure, mutation
or solvation, suitable to get e new set of perturbed charges requested to
define lambda. In the Gibbs manual, it seems possible to perform such a
calculation with PMF, however the documentation about it seems not really
complete, and hard to understand whether the change of the conformations as
to be done manually or not. If anybody has a concrete example or method
on how to solve this problem, that would be really great.

thanks so much for your time and attention

best regards

claudio

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