Hello Dr. Justin, So, the option "couple-intramol = yes" can be used to selectively turn off vdw and coulombic interactions of only few atoms from the rest of the molecule using a B state topology in Gromacs, as mentioned by Asaf.
On Thu, Dec 26, 2013 at 6:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. > -- *--------------------Thanks and Regards,Bipin Singh* -- 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.