[gmx-users] hessian calculation with periodic boundary condition
jtravers70 at yahoo.com
Mon Aug 12 15:49:36 CEST 2013
thanks. One more question, is there an easy way to ask gromacs to output the forces and the 2nd derivative? Or one has to modify the source code to do this?
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Sent: Sunday, August 11, 2013 12:17 PM
Subject: Re: [gmx-users] hessian calculation with periodic boundary condition
On 2013-08-11 17:00, John Travers wrote:
> I am trying to use gromacs to do hessian calculations for some of the structures along a trajectory. Do you know whether the normal mode analysis in gromacs takes into account the periodic boundary condition when computing the 2nd derivative? Thanks!
Yes it does. The parallel version is broken, by the way, a fix is underway.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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