Thanks. I do get LINCS warning all the time. I had removed two water molecule, that seemed too close to where the LINCS warning came for. And started the simulation again from the scratch and it stopped as mentioned in my previous message. Ragothaman --- Mark Abraham <[EMAIL PROTECTED]> wrote:
> Ragothaman Yennamalli wrote: > > Dear all, > > I am running a MD simulation, which stops after > 6ns > > run with an error saying: > > > > t = 6825.932 ps: Water molecule starting at atom > 19637 > > can not be settled. > > Check for bad contacts and/or reduce the > > timestep.Wrote pdb files with previous and current > > coordinates > > > > How does one proceed from here? Is removing the > single > > water molecule a solution? In that case wouldn't > there > > be a conflict between the number of atoms of > previous > > trr file and the new one being made? > > Yes, you can't continue from where you are. You > should have a close look > at what's been happening and see if there are any > other problems. > Probably you need a more gentle > minimization-equilibration regime at the > start. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
