The problem was solved by adding -pbc mol -ur compact flags to the trjconv. So the problems were indeed in pbc conditions
James 2013/5/3 Mark Abraham <mark.j.abra...@gmail.com> > On Fri, May 3, 2013 at 3:17 PM, James Starlight <jmsstarli...@gmail.com > >wrote: > > > Mark, > > > > > > but if I run npt equilibration onto minimized structure (without > > velocities) without definition of the new velocities in the npt.mdp file > > > > gen_vel = No > > > > I noticed that in npt.gro file velocities present. Have it been assigned > > inspite on > > gen_vel = No in mdp? > > > I can't answer - I don't know from your description and filename what was > in > 1) the coordinte file you input to the EM grompp, > 2) the .gro file you got out of EM mdrun (which presumably went into the > NPT grompp), > 3) the .tpr file you got out of NPT grompp, and > 4) the .gro file you got out of NPT mdrun (which will always have > velocities regardless of the foregoing) > > Please respect your reader's time and describe your observations carefully > :-) > > I think there should never be velocities in 2. Velocities in 3 should > follow what the .mdp file said (but if 2 wrote velocities, then it is > conceivable that those are still the velocities in 3 iff gen_vel=no, but > you would have to inspect the values with gmxdump to see what was > happening). > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists