On 4/25/17 10:35 AM, sp...@iacs.res.in wrote:
Hii all, I have simulated protein in 45% ethanol water mixture for 100ns. After completion of the job I saw that maximum portion of my protein goes out of the box. Then I have done trjconv -pbc mol to the trajectory file. After trjconv some portion of the protein is still out of the box. I want to see the local environment of the protein using the .gro file(last frame) but some portion of protein is dry. How can I get the actual state of protein after completion of 100ns?
You may need a few iterations of trjconv to get what you want. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
