Re: AMBER: Gibbs PMF Calculation

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Wed, 01 Feb 2006 07:54:33 -0500

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.
>
> Id 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
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Feb 02 2006 - 06:10:05 PST
Custom Search