On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > Dear Steven, > > Where are you working?
I work in UK, London. Why are you asking? > >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. I think I will just need a potential energy between those residues (LR and Coulombic) and then can get the effective potential Ueff=-kTln<e(-BU) and then g_dist. I want to extract parameters for coarse-grained simulation. Steven > 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 -- 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
