> From: makoto-yon...@aist.go.jp > To: gmx-users@gromacs.org > Date: Mon, 10 Jan 2011 23:57:46 +0900 > Subject: [gmx-users] truncated LJ potential > > Dear David and Hess: > > Thanks a lot for quick replies. > > >> please look into gromacs' table potential functionality, it is described > >> in the manual, and you won't have to program anything > >> UNLESS the sigma is different for different atom pairs, in that case I'm > >> not sure if it will work. > > The target system has many different atom types with different sigmas (and > epsilons). > I'd like to switch between the standard LJ potential simulation and the > corresponding > repulsion only one with the same LJ parameter sets for the real compounds > not simplified models. > > > You can make different tables for interactions between groups of atoms > with > > different sigma's by putting these groups in different energy groups, > > but this might get tedious. > > As the modification which I'd like to try is very simple one from the > original LJ function, I'd like to try to modify the code instead of > supplying > many kinds of the tables for each pairs of atom types. > > > You can also set the environment variable nb_generic.c and modify > > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat > > slower simulations. > > The LJ potential and force code in the above looks like in the c6-c12 form > not in epsilon-sigma one. > The LJ potential modification I'd like to try is based on the epsilon- > sigma form and the mixing rule is the Lorents-Bertelot's one. > Could you kindly tell me the LJ potential and force routine in the epsilon- > Sigma form. There is no such code. You can simply check for rinvsix > c6/c12. Berk > > Thank you for advance. > > Makoto Yoneya, Dr. > http://staff.aist.go.jp/makoto-yoneya/ > > -- > gmx-users mailing list gmx-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
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