Hi, I ran g_wham 4.5.2 and did get a non-zero PMF curve. I assume that there is something going on with g_wham on version 4.5.1.
Thank you for your help. Susana On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham <[email protected]>wrote: > On 10/03/2011 1:43 AM, Susana Tomasio wrote: > > Thank you Jianguo. > > So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1? > > > Quite likely. Check the change logs on the GROMCACS website for relevant > issues. > > Mark > > > > Best regards, > > Susana > > > > On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li <[email protected]> wrote: > >> I met the same problem when using 4.5.1 for some systems, the PMF shows >> zero curve, while the hist file looks fine. The problem disappears when >> using 4.5.2. >> Jianguo >> >> ------------------------------ >> *From:* Susana Tomasio <[email protected]> >> *To:* [email protected] >> *Sent:* Wednesday, 9 March 2011 20:07:25 >> *Subject:* [gmx-users] Zero Potential of Mean Force with g_wham >> >> Dear all, >> >> I am running umbrella sampling of a molecule through a lipid bilayer with >> gromacs 4.5.1. >> When I extracted the potential of mean force with g_wham I got zero for >> all the windows. >> Any ideas of why this is happening? >> >> This is the command I used: >> g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist >> >> And this is the pull code of my .mdp file: >> >> ; Pull code >> pull = umbrella >> pull_geometry = position >> pull_dim = N N Y >> pull_start = yes >> pull_ngroups = 1 >> pull_group0 = Bilayer >> pull_group1 = Protein >> pull_vec1 = 0 0 0 >> pull_init1 = 0 0 0 >> pull_rate1 = 0 >> pull_pbcatom0 = 1453 >> pull_pbcatom1 = 13187 >> pull_k1 = 3000 ; kJ mol^-1 nm^-2 >> pull_nstxout = 1000 ; every 2 ps >> pull_nstfout = 1000 ; every 2 ps >> >> Thank you. >> Best regards, >> >> Susana >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
