[gmx-users] hessian calculation with periodic boundary condition
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 11 18:17:19 CEST 2013
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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