On 9/14/14 8:43 AM, shahab shariati wrote:
Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer (bottom). I really do not know what thing has to be translated. Should I shift all components of my system (DPPC, drug, and water molecules) along z or only drug molecules?
Translate the whole system.
The dimensions of my system in final gro file are as follows: 6.46063 6.57889 8.30034 Based on your reply (The exact magnitude depends on the dimensions of the system), should I use following command: trjconv –trans 6.46063 6.57889 8.30034
If you used pressure coupling, no, because the box dimensions will change over time. Moreover, you do not want to change x and y. As I said before, you want to translate along z. Try a few values and see if you get a reasonable result.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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.
