[gmx-users] Tabulated Potentials

[O'Neill, David]

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