AMBER Archive (2004)

Subject: Re: AMBER: free energy profile calculation

From: David A. Case (
Date: Thu Jan 15 2004 - 10:32:17 CST

On Thu, Jan 15, 2004, David Smith wrote:
> That is, there may be a way to define a more flexible kind of restraint
> force in SANDER and calculate the PMF using some kind of histogramming
> technique. However, this is a bit beyond my area of expertise. Perhaps
> someone else would care to comment on this option.

This feature will be "automated" and documented in amber8. For current
versions, one would have to modify the (sander) code.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to