Hi guys > Sorry about the wrong subject in the previous e-mail. (I just hit reply). > I have been running gromacs for a few months now with no real problems > however some of my numbers differ from my supervisor's who uses DL-POLY. > Anyway discussion of the discrpnacies has led me to questioning aspects > of my topology file below (exerpts). We created the topology ourselves. > I always thought that the set up below would calculate 1-4 interactions, > but having read through the archives I am now confused. Do I have to > give a pair list in topology file, or is gen-pairs = yes sufficient. I > never created a pairlist as I thought that gen-pairs would create it > from the parameters 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 > > ;Molecular level > [moleculetype] > ; name nrexcl > subhexylcage 3 > > [atoms] > ; atomnr type resnr residue name cgnr charge mass > 1 CA 1 CGE CA 1 -0.1150 12.0110 > 2 CB 1 CGE CB 1 0.0000 12.0110 > > [bonds] > ; ai aj func b0(nm) kb(kjmol-1 nm-2) > 1 2 1 0.1400 392459.2 > 1 6 1 0.1400 392459.2 > > [angles] > ; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2) > 2 1 6 1 120.00 711.2800 > 2 1 7 1 120.00 292.8800 > > [dihedrals] > ; ai aj ak al func V1 V2 > V3 V4 (all kj mol-1) > 1 2 3 4 5 0.00000 30.33400 > 0.00000 0.00000 > 1 2 3 10 5 0.00000 30.33400 > 0.00000 0.00000 > > ;System level > [system] > ;the name of this system > config test of 32 subhexyl cage molecules > > [molecules] > ; moleculename number > subhexylcage 32 > >
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