Dear Gromacs user, Below are the result of PMF simulation of a peptide adsorbed into a solid surface. Would you please comment on them in order to improve the result.
The force constant in the umberela sampling is 1100. For each windows: 1.2 ns NVT equilibration followed by 2 ns of NPT and 15 ns of NVT produciton run. Should I change the force constant or increase the simulation time for each windows or just increasing the sampling in some region? https://drive.google.com/open?id=0B_CbyhnbKqQDMkpLc0didlMxTWs https://drive.google.com/open?id=0B_CbyhnbKqQDZ1RpT3JxMjdyazA https://drive.google.com/open?id=0B_CbyhnbKqQDZlR4RGVIWk5KbVU It is just one dimension pulling by "N N Y" by pull-coord1-geometry = distance, then I was also wondeing why my pullx.xvg files has more than normal column so that gmx wham complain with error about it: Fatal error: Using 1 pull coodinates from prdd.0.tpr, but found 4 data columns in pullx-prd.0.xvg (expected 3). Thanks very much in advance. Regards, Alex -- 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.