AMBER Archive (2004)

Subject: Re: AMBER: PMF

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Oct 25 2004 - 07:14:19 CDT

the spring constant is the one that you used to restrain each simulation to
a particular range of reaction coordinate. you'll also want to check to
see if
5 simulations is enough to cover your reaction coordinate with sufficient
overlap between windows.
if you're not sure how this works, you should probably read more articles
where umbrella sampling is described.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
==================================================================

tang kwa wrote:

>Dear all,
>
>I have a question about umbrella sampling.I performed
>five independent simulations to create the history
>files of the angle along the trajectoris. I have used
>the same input in the manual (P.137)
>In the next step, I used WHAM program to evaluate the
>free energy.I have to give the the spring constant to
>be a input file for this program.I get different
>minimum point if I change the spring value.
>
>Could anybody give me an advise? How can I select the
>value of the spring constant?
>
>Best wishes,
>TK
>
>
>
>
>
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