AMBER Archive (2004)

Subject: Re: AMBER: user force

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Jul 23 2004 - 06:47:17 CDT

it's possible to do many kinds of umbrella sampling already by using the
nmropt distance, angle and dihedral restraints. you can also use RMSD
restraints. it might help us to know what kind of extra umbrella potential
you want to add. then we could be more specific about how to add it.

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant 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
===================================================================

myunggi_at_csit.fsu.edu wrote:

>Thank you Carlos and Ross,
>I'm using Amber7 version on a Linux cluster.
>I want to get umbrella sampling for PMF by adding my own bias function(al form)
>to five Amber force fields. So I'll keep the all Amber force field. I will add
>only one more term to Amber force field. That's it.
>Is it the only way to modify the source code?
>Even though I'm an experienced, the source codes are so complicated.
>What about the version 8 ?
>
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