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.
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.
