yes it will... On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh <[email protected]> wrote:
> 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 >
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