Presumably this is with a standard, non-modified forcefield. One thing that might be worth trying (as, perhaps, a last resort) is reducing the timestep. It's a bad thing to have to do, because it reduces speed massively, but might help equilibrate your system and reduce whatever bad contacts are causing the problem. You could then crank up the timestep again to something more productive. Running at a lower temperature for a while, again, might allow the system to settle down.
--- Ashutosh Jogalekar <[EMAIL PROTECTED]> wrote: > Hello > I am simulating a regular seven residue peptide: > HHQALVFFA, in the > form of a beta sheet with five strands. > The EM went ok. The structure looks ok. But I am > still getting the > error about the LINCS constraint deviation during > the posit. restr. MD. > Could someone suggest what I could do to get rid of > the problem? > dt= 0.002 > nsteps= 10000 > constraints= all-bonds > tau_p= 1.0 > > Thanks > Ashutosh Jogalekar > Emory University > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
