On 4/4/17 2:42 AM, 吴萌 wrote:
Hi All, I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to add some substrate molecules(acetate) to my system, and I used this command: "gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb -o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz", but then I found many acetate molecules are put out of the system in the out .pdb. Is that normol or wouldl affect the later MD process? If so, how can I fix it. Any suggestions would be greatly appreciated. Thank you in advance!
There's no such thing as "outside" of a periodic box. -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.
