My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus
I have tried all combinations of "trjconv -pbc -center -box center" and nothing works..I was able to get online and find a tutorial that says trjconv -pbc mol, should stop the problem, but this failed....Isn't there a way for the protein and water to be wrapped or COM calculations done DURING MD to remove translation, rotation so that post-MD modification of trajectories is unnecessary??...If I make an index group of the N-terminus of the protein this problems goes away or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)....Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up.... Thanks, Steve -- 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.
