On 11/6/14 4:53 PM, Chris Papamitrou wrote:
I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the pdb2gmx -f input.pdb -ignh -ter -o complex.gro command and was wondering what effect that the -ignh option had on my simulated results? do the hydrogens not get accounted for in this simulation, and if so, how are the atomic bonds in which the hydrogens are supposed to be located treated in terms of replacing those hydrogens? does this mean i am doing a united atom model ?
Start with pdb2gmx -h. The -ignh has a very simple purpose, and it's used mostly for working around nomenclature issues.
Whether or not you use a united-atom force field is entirely up to you, based on what you choose.
-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 [email protected] | (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 [email protected].
