Cheers Sikandar I take it that because combination rule 3 (provide sigma and epsilon) is stated gromacs assumes that all values in nonbonding parameters are sigma and epsilon. I know this tp be tru for the atomtypes but does it filter down to all intermolecular interactions.
Cheers Gavin Sikandar Mashayak wrote: > Yes, since sigma and epsilon are zero for VS then interactions between > and VS-VS and VS-(any other atom) would result in zero force. Since > you explicitly define the interaction between VS-C3, combination rule > won't be used and C6(VS_C3) and C12(VS_C3) will be computed as per > sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params] > > cheers > > sikandar > > On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh <[email protected] > <mailto:[email protected]>> wrote: > > Am I correct in saying now, from the following topology (exerpts), > that > the virtual site VS will only interact with C3? > I guess I don't have to give the atom indices of this interaction > in the > pair list which I use only for 1_4 interactions? > Can I use sigma and epsilon in the nonbond_params directive like in > atomtypes. > > ;Parameter level > [defaults] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 3 yes 0.5 0.5 > > [atomtypes] > ;type mass charge ptype sigma(nm) > epsilon(kjmol-1) > CB 12.011000 0.000000 A 0.355000 0.292880 > CA 12.011000 -0.115000 A 0.355000 0.292880 > HC 1.008000 0.115000 A 0.242000 0.125520 > CU 13.019000 0.265000 A 0.350000 0.334720 > NU 14.007000 -0.597000 A 0.325000 0.711280 > CH 13.019000 0.332000 A 0.385000 0.334720 > C3 15.035000 0.000000 A 0.390500 0.732200 > C2 14.027000 0.000000 A 0.390500 0.493712 > VS 0.0 0.0 V 0.0 0.0 > > > [nonbond_params] > ;i j func sigma epsilon > VS C3 1 0.1 0.03153 > > -- > gmx-users mailing list [email protected] > <mailto:[email protected]> > 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 [email protected] > <mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
