Hi again To rephrase. If I have two atoms constructing a charge group, is it not possible to have one of these atoms constructing an energy group on its own?
Cheers Gavin Gavin Melaugh wrote: > Hi All > > I have set up a topology file and with virtual sites (exerpts below), > whereby my virtual sites only interact with the C3 atoms. I am trying to > construct a PMF wrt one particular C3. This atom I do not want to > interact with the virtual sites at all. I thought the best way to do > this was via energy exclusion groups. So I set up some groups in the > index file (see below), and defined the energy groups like so > energygrps = vsites vsitex > energygrp_excl = vsites vsitex > > but I get the following error > > Fatal error: > atoms 415 and 416 in charge group 89 of molecule type 'name' are in > different energy groups > I have no charge group 89 in my molecule. Can someone please suggest > where I might be going wrong. > > ;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 0.391000 0.669440 > C2 14.027000 0.000000 A 0.390500 0.493712 > VS 0.0 0.0 V 0.0 0.0 > > [nonbond_params] > ;i j funct sigma epsilon > VS C3 1 0.1 0.03153 > > > [ cage_1 ] > 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 > 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 > 61 75 89 103 117 131 145 159 173 187 201 215 > [ tail ] > 416 > [ vsites ] > 229 230 231 232 461 462 463 464 > [ vsitex ] > 416 > > -- 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
