[gmx-users] hessian calculation with periodic boundary condition

[David van der Spoel]

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