On 2/22/14, 12:43 PM, Nikhil Agrawal wrote:
Hi All, I have simulated a membrane proteins system using coarse grain model. after simulations when i removed periodic boundary from my simulations box but the protein is moving up and down in the box ? I have tried all the options nojump ,mol,whole ...etc. no options seems to work.
Without the exact sequence of commands, it's not possible to suggest where you might have gone wrong. Note that multiple passes to trjconv are typically necessary.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
there is something wrong with my trajectory or it is normal with CG ?
Periodicity effects do not depend on the force field. It is certainly possible that your box is too small for the system being considered, thus the PBC algorithms in trjconv can't reconcile things (and in that case, your trajectory would suffer from minimum image violations). What are the dimensions of your box, and how much space exists between the protein and the box edges?
-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.
