Dear Steven, Where are you working?
>From my experience the g_energy -fee only gives a free enrgy estimate for the >whole system, so one has to pull out all the energy terms based on your index >file of interest and sum them in a spread sheet. if the -fee can do the >energy estimates for a specific set, please let me know this would be valuable >to me. Sincerely, Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 28 Jun 2012 09:28:09 +0100 > Von: Steven Neumann <s.neuman...@gmail.com> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: [gmx-users] Free energy between residues > Dear Gmx Users, > > I want to obtain the free energy difference between the pair of > residues in my protein chain with respect to thheir distance. Would > combinbation: > > 1) g_dist - distances between two groups during the simulation time > > 2) g_energy -fee (DelatG - with energy groups I am interested in > stated in mdp file) > > give me those values? > > Or I should use PMF - umbrella sampling with the bias (harmonic) > potential introduced? > > Thank you, > > Steven > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
