AMBER Archive (2006)

Subject: Re: AMBER: Gibbs PMF Calculation

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Feb 01 2006 - 06:54:33 CST

people don't use gibbs much anymore, I'd suggest using
sander to do this. since the atoms aren't changing you
don't need any perturbation defined, you might try umbrella
sampling.

Atsutoshi Okabe wrote:
>
> Dear,all.
>
> I’d like to use Gibbs to calculate free energy varing
>
> the distance between two molecules, for example two methanes in water.
>
> In this case,do I need to set particular perturbed atoms or perturbed
> charges
>
> And to execute saveamberparmpert command in tleap?
>
> Could you give me a suggestion?
>
> Thank you.
>
> Atsutoshi Okabe
>
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