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On 8/29/16 6:16 AM, Seera Suryanarayana wrote:
Sub: Segmentation fault Dear Justin and Vivek, I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have through the many references for refcoordscale, despite of some information I am not getting what exactly it is? Kindly give me some hit.
The pressure coupling scaling matrix adjusts atomic positions in response to variations in pressure. If you use a fixed reference as the origin of the position restraints, you will get a systematic drift in that position with respect to the coordinates propagated during dynamics. So with the refcoord_scaling option, the reference coordinates (e.g. those at t=0, usually) have the same scaling matrix applied to them so that you don't get spurious contributions that might distort the structure. The "com" option scales relative to the center-of-mass of the restrained group(s), whereas "all" scales every atom individually. I find "com" to generally be the best option.
-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.
