On 12/25/13, 4:55 AM, Asaf Farhi wrote:
Dear all Hi. We have a question regarding the implementation of free energy calculations in Gromacs that we have been trying for long time to decipher. The question is the following: When transforming molecule A to B if the non bonded interactions are changed through the topology file e.g: [ atoms ] ; nr type resnr resid atom cgnr charge mass typeB chargeB massB 1 HC 1 PCH3 H1 1 0.123 1.0080 HC 0.0 1.0080 , will the the interactions of this atom with all the other atoms be affected by this change of charge?
That depends on how you are setting coupl-intramol (and on a related note, check out http://redmine.gromacs.org/issues/1340). The nonbonded interactions between the coupled molecule and its surroundings are affected. Whether or not intramolecular interactions are affected depends on coupl-intramol.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.