Hi, On Tue, Jan 5, 2016 at 7:26 AM Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > On Tue, Jan 5, 2016 at 4:46 AM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/4/16 10:41 PM, Pallavi Banerjee wrote: >> > Hi Mark, >> > >> > Thank you for your reply. >> > >> > I want to implement this wacky idea because a part of the potential of >> the >> > system needs to be input in a tabulated form (referring to Iterative >> > Boltzmann Inversion) and the other part (solvent-solvent) interaction is >> > defined by sigma and epsilon, which I again input in the form of a table >> > since GROMACS does not support both tabulated and non-tabulated at the >> > same time. >> > >> > So, then, am I right to understand that eqn 4.28 of manual-5.1 is the >> > functional form of potential of the force-switch method, and that there >> is >> > no documentation provided for potential-switch? >> > >> >> It may not be in the GROMACS manual, but is it not the same as what is in >> Steinbach and Brooks JCC (1994) 15: 667-683, like the force-switch is? >> This is >> the CHARMM potential switching, which should be the same, IIRC. >> > > Thanks, but > https://github.com/gromacs/gromacs/blob/master/src/gromacs/gmxlib/nonbonded/nb_generic.cpp#L137 > suggests > they are not the same. > I did some cranial archaeology upon Erik, which led me to commit 4e61f8f4b26da, which led me to https://github.com/gromacs/gromacs/blob/master/src/gromacs/tables/forcetable.cpp#L961. The potential-switch function is indeed in the spirit of Steinbach & Brooks, but smoother because it has higher-order continuity. Several others have also implemented switching functions in this way. (But I don't think anybody now recommends you use it for Coulomb...) I've documented the potential-switch modifier for the upcoming 5.1.2 release - see https://gerrit.gromacs.org/#/c/5526/ Mark -- 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.
