Re: [gmx-users] How to exclude the interactions between molecule A and B in Gromacs?
On 5/08/2011 1:17 PM, DeChang Li wrote: Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus's group (J. Am. Chem. Soc. (1990) 112, 9161-9175. & J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. See energy groups and energy group exclusions in 3.3 and 7.3.19 of the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?
Dear all, I want to use Gromacs to run an enhanced sampling molecular dynamics (ESMD) proposed by Karplus’s group (J. Am. Chem. Soc. (1990) 112, 9161-9175. & J. Mol. Biol. (1999) 291, 101-115). In the ESMD simulation, we need to exclude the interactions (especially the Coulomb interactions) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. Best regards, = Dechang Li, Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China = -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
