Re: [AMBER] free energy calculation with TI

From: <>
Date: Wed, 16 Mar 2011 05:21:52 -0400 (EDT)


> For the vdw-removing step of solvation free energy calculation,
> prmtop/inpcrd files of V0 and V1 are solute+watbox and watbox_only. In
> addition, scmask of V0 should specify all the atoms of the solute. Is that
> correct?

yes that is correct. You would probably also set crgmask=scmask in V0 to
disappear the atoms without charges.

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Mar 16 2011 - 02:30:03 PDT
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