On 10/29/14 6:32 AM, Kester Wong wrote:
Dear all, I am creating a topology file for hydroxide, closely following the parameters from the paper by Wolf et al: http://dx.doi.org/10.1016/j.bpj.2014.04.062 This is somewhat similar to the polarisable hydroxide topology that was included in the recent SWM4-NDP force field. In this non-polarisable topology, I would like to know what atomic number should one label for the OH-OV2 type atom, as it was defined as a virtual site (but with 1 a.m.u assigned) in the paper's supporting material. I have labeled the atomic number with "X" as below: [ atomtypes ] ;name at.num mass charge ptype sigma epsilon OH-O 8 11.9980 -1.32 A 0.00 0.00 OH-H 1 1.00800 0.00 A 0.14 0.2150576 OH-OV1 0 0.00000 0.00 D 0.2916 0.2150576 OH-OV2 X 1.00000 0.00 A 0.25 0.2150576 OH-qH 0 0.00000 0.32 D 0.00 0.00 Can an atom (ptype=A) have zero at.num?
I would suggest you simply ask the authors to provide you with their topology. There are several details that are unclear to me, and I do not see anything that says the V1 or V2 sites carry any mass. Maybe I missed it due to a quick read-through, but this is in any case a very tricky setup. Don't reinvent the wheel; get the information straight from the people that did it.
-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.
