AMBER Archive (2005)

Subject: Re: AMBER: PMF calculations with TI using the sander

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 18 2005 - 11:03:47 CDT

On Mon, Jul 18, 2005, Vitor Manuel Sousa F?x wrote:
>
>
> I am interrested to investigate the reaction path
> associated with the entry of the metal ion into the
> macrocycle cavity via PMF coupled with TI. I would like to
> know if is possible to undertaken this type of calculation
> with sander or only with Gibbs ?..

I'm not sure what sort of simulation you have in mind, that would combine
calculating a PMF (which measures free energy for a conformational change)
and TI (which generally measures free energy when the potential energy
function is being changed.) I don't know of any reason why sander would
object to combining the two, but the analysis might be fairly tricky.

....dac

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