Re: [AMBER] PMF for dimer dissociation

From: Carlos Simmerling <>
Date: Tue, 17 Mar 2015 19:25:07 -0400

what are the monomers? how difficult will it be to keep them rigid?

On Tue, Mar 17, 2015 at 5:18 PM, Sanmeet Chahal <> wrote:

> Hello All,
> I need to compute a PMF for the dissociation of a dimer in TIP3P water. I
> need each dimer to remain 'rigid' from an intramolecular and relative
> standpoint. My PMF transformation is simply moving only one monomer away
> from the other monomer with a simple translation of their atoms. The goal
> of this calculation is to mimic a PB-type PMF along the separation axis but
> now with proper statistics and explicit solvent.
> I thought that thermodynamic integration would be the right formalism for
> this in AMBER (though umbrella sampling could be more efficient).
> What is the best way to compute this PMF calculation in AMBER? Any example?
> Thanks,
> Sanmeet
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Received on Tue Mar 17 2015 - 16:30:02 PDT
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