[gmx-users] hessian calculation with periodic boundary condition

John Travers jtravers70 at yahoo.com
Wed Aug 14 03:10:55 CEST 2013


Do you know whether the Hessian in Gromacs is computed analytically or numerically? From the manual (Page 52), it seems it is  computed by finite difference method. Is it the case in Gromacs 4.6.3? Thanks



 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:
> Hi,
> 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!
> Best
> JT
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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