Hi, 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
Best JT ________________________________ From: David van der Spoel <sp...@xray.bmc.uu.se> To: gmx-users@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. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
