Hello Users, Recently I have been trying to implement the use of tabulated potentials in GROMACS to an system of argon atoms.
I run a NVE simulation of 1000 argon atoms and then plot the potential energy from the output. ar.itp : [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon Ar 18 39.94 0.000 A 0.34 0.997 [ nonbond_params ] ; i j func c6 c12 Ar Ar 1 0.34 0.997 Then I run the same simulation but with tabulated potentials. ar.itp: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon Ar 18 39.94 0.000 A 1.000 1.000 [ nonbond_params ] ; i j func c6 c12 Ar Ar 1 1.000 1.000 The mdp file has changes of: xtc-grps = ; Selection of energy groups energygrps = Ar energygrp_table = Ar Ar coulombtype = user vdw-type = user My table file (table_Ar_Ar.xvg) looks like this: 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 5.0000000000e-04 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.5000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 2.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 2.5000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 ........................................................................................................................................................................................................... ........................................................................................................................................................................................................... 1.0000000000e-01 1.0000000000e+01 1.0000000000e+02 -6.1606800110e+03 -3.6964080066e+05 9.5170456866e+06 1.1420454824e+09 1.0050000000e-01 9.9502487562e+00 9.9007450311e+01 -5.9790513233e+03 -3.5695828796e+05 8.9641561500e+06 1.0703470030e+09 1.0100000000e-01 9.9009900990e+00 9.8029604941e+01 -5.8036392503e+03 -3.4477064853e+05 8.4458948214e+06 1.0034726520e+09 1.0150000000e-01 9.8522167488e+00 9.7066174865e+01 -5.6342018047e+03 -3.3305626432e+05 7.9599373058e+06 9.4107633173e+08 1.0200000000e-01 9.8039215686e+00 9.6116878124e+01 -5.4705075446e+03 -3.2179456145e+05 7.5041255756e+06 8.8283830301e+08 1.0250000000e-01 9.7560975610e+00 9.5181439619e+01 -5.3123350657e+03 -3.1096595506e+05 7.0764553285e+06 8.2846306285e+08 ........................................................................................................................................................................................................... ........................................................................................................................................................................................................... 1.8975000000e+00 5.2700922266e-01 2.7773872077e-01 -1.3198906261e-04 -4.1735671970e-04 4.3683833118e-09 2.7626139521e-08 1.8980000000e+00 5.2687038988e-01 2.7759240774e-01 -1.3178057657e-04 -4.1658770253e-04 4.3545938718e-09 2.7531678852e-08 1.8985000000e+00 5.2673163023e-01 2.7744621029e-01 -1.3157247463e-04 -4.1582030435e-04 4.3408515750e-09 2.7437565921e-08 1.8990000000e+00 5.2659294365e-01 2.7730012831e-01 -1.3136475599e-04 -4.1505452131e-04 4.3271562481e-09 2.7343799356e-08 1.8995000000e+00 5.2645433009e-01 2.7715416167e-01 -1.3115741984e-04 -4.1429034960e-04 4.3135077182e-09 2.7250377793e-08 1.9000000000e+00 5.2631578947e-01 2.7700831025e-01 -1.3095046538e-04 -4.1352778540e-04 4.2999058130e-09 2.7157299872e-08 The potential energy is then plotted, but they are different for each system when they should be the same. I have spent quite some time on this checking the files looking for what I have done wrong, it is clear to me that it might be rather obvious but I just can't see it as I'm too far in. Anyone see my mistakes? Regards, Stream -- 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
