[gmx-users] about using both Lennard Jones and Buckingham potential

Santosh Kumar Meena s.kumarmeena at sheffield.ac.uk
Fri Nov 23 16:15:23 CET 2018

Dear all,

I tried to use Lennard Jones and Buckingham potential together using
tabulated potential for my system as follow as descried in the document (

please see below part of my topology file where in nonbond_params section
attractive C6 parameter C and repulsive parameter A of Buckingham potential
are written
 and for the rest of pair C6 and C12 parameters of Lennard Jones potential
are written.

table of the each pair of LJ and Buckingham is prepared as follow:
               r       f(r)         -f'(x)             g(r)
-g'(r)                h(r)            -h'(r)

       r,       1/r,       1/(r*r),          -1/(r**6),   -6/(r**7),
1/(r**12),             12/(r**13)

          r,      1/r,     1/(r*r),             -1/(r**6),
-6/(r**7),       exp(-B_OM_OW*r), B_OM_OW*exp(-B_OM_OW*r)

where bellow tables are in the folder
table.xvg table_CA_OM.xvg  table_OM_H.xvg   table_OM_OW.xvg
 table_CA_C.xvg  table_CA_OW.xvg  table_OM_OM.xvg  table_OW_OW.xvg

and i put below option minim.mdp file

coulombtype  =  PME
cutoff-scheme = group
vdw-type = user
energygrps = CA C OM OW H
energygrp_table = OM OW OM H OM OM CA OM CA C CA OW OW OW

*I am getting large LJ force and large LJ potential and a message that one
or more water molecule can not be settled so i am not able to minimize my
system, however this forcefield working fine in DL_poly as there are option
to include LJ and Buckingham both at the same time.*

*Could you please help me where i am wrong or there is inherent problem in
gromacs in including like this LJ and bucking potentials?*

[defaults ]
; nbfunc   comb-rule   gen-pairs   fudgeLJ   fudgeQQ
  1          1             no       .5     0.8333

[ atomtypes ]
; name   bond-type   mass   charge   ptype     C [simg nm]   A [epsilon
   CA      20        40.078     0          A        0               0
   C        6         12.0110   0          A        0                 0
   OM       8         15.9994   0          A       0                 0
   OW       8        15.9994   -0         A        0                0
   H        1           1                 0              A
0              0

[ nonbond_params ]
; i      j   func            C              A
  OM   OW    1          0                 1209391.22
  OM    H    1            0                    38237.13
  OM    OM   1         2.692e-3                  6159641.2313
  CA    OM   1            0                      305051.18045
  CA    C    1               0                      1157823690
  CA    OW   1            0.0005045            7e-7
  OW    OW   1         2.6171e-3          2.634e-6

Dr. Santosh Kumar
Research Associate
Department of Materials Science and Engineering,
University of Sheffield
Sir Robert Hadfield Building
Mappin Street, Sheffield, S1 3JD
san.iitb at gmail.com <pchuy1906 at gmail.com>
s.kumarmeena at sheffield.ac.uk <pchuy1906 at gmail.com>
Mobile: +447470768115

Website: https://realworldcrystals.leeds.ac.uk/
Twitter:   https://twitter.com/Realworldxstals

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