Mark, thanks for suggestions
as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings 2013/5/3 Mark Abraham <mark.j.abra...@gmail.com> > Trajectory frames written by mdrun are not post-processed to guess how you > would like PBC to be treated for whatever purpose you have next. So if a > molecule straddles a periodic boundary given the current center position, > that's what it looks like. If there are things you want to do, then there's > the instructions at > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > . > > In turn, it seems grompp applies a whole collection of basic checks, and it > seems that one of them might not be sufficiently PBC-aware. Such checks > appropriate for a normal grompp workflow, where this is the first point the > GROMACS machinery gets to see what you intend to do and is the point where > it can help you ensure sanity. It seems there's room for a small > improvement, too. > > If the subsequent MD works, then you need have no concern, but if you want > to post-process your trjconv frames so that the molecules are whole, you > will suppress this warning the "correct" way. > > Mark > > On Fri, May 3, 2013 at 8:18 AM, James Starlight <jmsstarli...@gmail.com > >wrote: > > > Dear Gromacs users! > > > > I have performed long md run. From the production trajectory by means of > > > > trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # > extract > > conformers from first 300 ps each 10ps steps > > > > > > I've extracted 10 conformers in the desired time step > > > > Than when I perform MD on each conformer I obtain error (when I loaded in > > grompp conformer from the initial run I have no such error) > > > > Number of degrees of freedom in T-Coupling group rest is 130551.00 > > Largest charge group radii for Van der Waals: 8.895, 7.586 nm > > Largest charge group radii for Coulomb: 8.895, 8.474 nm > > > > WARNING 1 [file ./mdps/minim.mdp]: > > The sum of the two largest charge group radii (17.368397) is larger > than > > rlist (1.000000) > > > > > > Finally after minimization of each conformer with the same R_list (with > > maxwarn 1 flag) and starting new MD on the minimizing conformer I have no > > such error: > > Largest charge group radii for Van der Waals: 0.241, 0.237 nm > > Largest charge group radii for Coulomb: 0.241, 0.237 nm > > > > Why this error have occurred (with no minimized conformers) and how it > > could be fixed correctly ? > > > > James > > -- > > 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 > -- 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
