On Wed, May 22, 2013 at 8:05 PM, rajat desikan <rajatdesi...@gmail.com>wrote:
> Thanks for the reply, > trjconv does not have any bugs in removing pbc, right? We can just feed the > -nojump output to g_msd. > Maybe. There are not (yet) any automated tests for the code in these tools. But probably trjconv -nojump works correctly else we'd have heard more screaming... Mark I am going to output the coordinates and velocities with g_traj and run it > through my own code :) > > > On Wed, May 22, 2013 at 11:19 PM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > Along the lines of take a trajectory, and look through it for a frame > where > > it crosses the periodic boundary of the original cell. Look for artefacts > > in the analysis at that time. Or take that frame and use it as a > reference > > state for whatever trjconv-based PBC-massaging workflow you previously > used > > before your analysis. > > > > How best to test depends exactly what you're measuring. There are too > many > > combinations in most GROMACS tools for one test to prove the whole tool > > works correctly (or even agrees with how you think it works), so you need > > to think about the context that matters to you. You can probably get > > creative with editconf's translation options and come up with some fake > > trajectories via trjcat that test some edge cases relevant to what you > want > > to do. > > > > Mark > > > > > > On Wed, May 22, 2013 at 7:40 PM, rajat desikan <rajatdesi...@gmail.com > > >wrote: > > > > > Hi Mark, > > > Regarding your statement, how does one check whether g_msd has removed > > pbc > > > correctly or not? > > > Thanks > > > > > > > > > On Wed, May 22, 2013 at 10:56 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > >wrote: > > > > > > > On Wed, May 22, 2013 at 4:49 PM, Yutian Yang <yyan...@syr.edu> > wrote: > > > > > > > > > Erik, > > > > > > > > > > Do you mean that if the particle diffuses too fast, it will appear > > like > > > > it > > > > > doesn't move because of the PBC? > > > > > > > > > > > > > Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect > > > > > > > > I have another issue. If I have a polymer chain with the length > almost > > > the > > > > > same as the box length. It is possible that the COM diffusion of > the > > > > chain > > > > > may appear it does not move or move backward due to PBC, right? > > > > > > > > > > > > > Depends how you've post-processed your trajectory and/or the GROMACS > > tool > > > > treats PBC. There have been bugs in the latter. Nobody's issued any > > > > warranties, so everyone should certainly be checking a) that the tool > > > works > > > > they way they think it does, and b) that the tool gives the right > > answer > > > on > > > > a relevant test case. Or the world may end when some reviewer points > > out > > > an > > > > analysis artefact some dark day... > > > > > > > > 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 > > > > > > > > > > > > > > > > -- > > > Rajat Desikan (Ph.D Scholar) > > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > > Dept. of Chemical Engineering, > > > Indian Institute of Science, Bangalore > > > -- > > > 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 > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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? 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