Dear all,<br><br>I am running umbrella sampling of a molecule through a lipid bilayer with gromacs 4.5.1.<br>When I extracted the potential of mean force with g_wham I got zero for all the windows.<br>Any ideas of why this is happening?<br>
<br>This is the command I used: <br>g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist<br><br>And this is the pull code of my .mdp file:<br><br>; Pull code<br>pull = umbrella <br>pull_geometry = position <br>
pull_dim = N N Y <br>pull_start = yes <br>pull_ngroups = 1 <br>pull_group0 = Bilayer <br>pull_group1 = Protein <br>pull_vec1 = 0 0 0 <br>pull_init1 = 0 0 0 <br>
pull_rate1 = 0 <br>pull_pbcatom0 = 1453 <br>pull_pbcatom1 = 13187 <br>pull_k1 = 3000 ; kJ mol^-1 nm^-2<br>pull_nstxout = 1000 ; every 2 ps<br>pull_nstfout = 1000 ; every 2 ps<br>
<br>Thank you.<br>Best regards,<br><br>Susana<br>