Hi, That would generally suggest something divided by zero, or similar, eg because no data was in a histogram bin, etc.
That behavior is a bug that we could perhaps fix if you would be so kind as to report it at https://redmine.gromacs.org. But the core problem remains that something about how you sampled didn't meet the expectations of gmx wham. Mark On Wed, Mar 14, 2018, 15:45 Ben Tam <btam...@hotmail.co.uk> wrote: > Dear all, > > I have a rather strange problem. Currently I am trying to get a PMF of a > water molecule through a hydrophobic materials. At the end of using "gmx > wham", I get a rather good histogram and it cover the whole range of the > system. However at the making profile.xvg. I get the answer "nan" inside > the file. Therefore I really cannot think of why is it giving me that? > > Currently I set it as : > ;Pull code > pull = yes > ;pull-cylinder-r = 0.5 > pull_ngroups = 2 > pull_ncoords = 1 > pull_group1_name = SOL > pull_group2_name = MOL > pull_coord1_type = umbrella ; harmonic biasing force > pull_coord1_geometry = direction-periodic ; simple distance increase, > direction-periodic > pull_coord1_vec = 1 1 1 > pull_coord1_groups = 1 2 > pull_coord1_dim = Y Y Y > pull_coord1_rate = 0.00 ; 0.01 nm per ps = 10 nm per ns > pull_coord1_k = 10000 ; kJ mol^-1 nm^-2 > pull_coord1_start = yes ; define initial COM distance > 0 > > Also this appears when I used the command "gmx wham": > > Switched to exact iteration in iteration 1 > 1) Maximum change -1.000000e+20 > Converged in 2 iterations. Final maximum change -1e+20 > > Therefore I really don't understand what I have to do in order to get a > profile.xvg. I understand the k value is high, but without that high value, > the water won't settle within the assign window. > > Am I doing something wrong? because I got a good histogram but no result > in the profile.xvg? Thank you very much for your help. > > Best regards, > > Ben > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.