On Sun, Feb 2, 2014 at 5:09 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 2/2/14, 7:15 AM, Atila Petrosian wrote: > >> Dear Justin and Tsjerk >> >> you said " Some tools handle PBC properly, some don't ". >> >> I want to know exactly which tools of gromacs handle PBC properly. >> >> Can I find these tools in manual? >> >> > No, because it's not possible to test every single command that the user > might issue and keep a reliable database of such information. True, but there is some partial information available - see e.g. known problems under genbox -h. It would certainly be a Herculean task to curate testing, documentation and/or fixing all such issues, though! Mark > > I did simulation of a system containing protein and cnt using gromacs >> 4.5.6. >> >> When I see trajectory by VMD, in some frames, protein atoms exit one side >> of box >> and enter opposite side of box. I want to do analysis of trajectory. I do >> not know >> exactly this state is pbc problem or not. >> >> > Again, that depends entirely upon the command you're using. Tools like > g_rms have problems when molecules are split across PBC. Other tools like > g_dist or g_msd handle the situation better. If the protein is the only > problematic molecule, it should be rather trivial to fix the PBC issues > with trjconv -center, trjconv -pbc nojump, trjconv -pbc mol -ur compact, or > trjconv -fit translation, or perhaps some sequence of those. Please refer > to the PBC link I have posted several times this week. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.