To make this clear, center the trajectory on the water and watch the time evolution in some visualization program.
Mark On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/27/13 12:05 PM, shahab shariati wrote: > >> Dear Tsjerk Wassenaar >> >> Very very thanks for your reply. >> >> I used trjconv -pbc mol. >> >> pbc problem was solved only for lipid molecules. >> >> When I see new trajectory by vmd, there are some problesm about drug >> molecule. >> >> https://www.dropbox.com/s/**xq4s6az17buhvb8/images-2.docx<https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx> >> >> If I show my system as 4 regions, my system before equilibration is as >> fallows: >> >> region (1): water + drug >> region (2): top leaflet of bilayer >> region (3): bottom leaflet of bilayer >> region (4): water >> >> After equilibration, drug molecule exits region (1) and enters region (4), >> alternately. >> >> On the other hand, drug molecule is in region (1)in some frames and is >> in region (4) in other frames. >> >> Please tell me how to fix it? Is this issue (about drug molecule) pbc >> problem? >> >> > As has already been stated several times, there is no problem at all. The > outcome is completely normal, and there are not discrete regions (1) and > (4). It is a continuous block of water via PBC. The molecule can freely > diffuse throughout it. > > -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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
