[gmx-users] Re: Tabulated Potentials

[Andrish Reddy]

O'Neill, David wrote
> 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
> 
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Try changing your comb-rule to = 1  in the [defaults] directive. Check
whether dispersion correction (if applied) is consistent with your new
tabulated potential. 

Andrish



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