On 29 February 2016 at 08:48, SAPNA BORAH <sapnauser...@gmail.com> wrote:
> hi > Thanks for the suggestion. I will give this a shot, and remove these > restraints. > > I am unclear about what should I be looking in the log file as you > mentioned. The conformations are not just close, they are the same as the > initial conformation. > See if you can find "Position rest." in your logfile in the Energies subsection. > > I have some understanding on pbc that serves a problem in visualisation of > the trajectory. I have applied the all sorts of pbc options, but somehow > things are not falling into place. If you could post a screenshot of what it looks like that would be handy. Currently there's not much else I can tell you. > > However the problem more grave here, for me, is the production run and the > model stability that is happening throughout the simulations in different > versions. > > The model stability is probably caused by the postion restraints. If you're telling gromacs to apply a restraint that penalizes movement of your atoms, it makes sense that you won't be seeing much movement. -- 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.
