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

Santosh Kumar Meena s.kumarmeena at sheffield.ac.uk
Fri Nov 23 15:12:18 CET 2018


Dear all,

I tried to use Lennard Jones and Buckingham potential together using
tabulated potential for my my system as follow as descried in the document (
http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf)

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

cutoff-scheme = group
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
water molecule are not settled so i am not bale to minimize my system,
however this forcefield working find in DL_poly as there are option to
include LJ and Buckingham at the same time.*

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


[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
kJ/mole]
   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
E-mail:
san.iitb at gmail.com <pchuy1906 at gmail.com>
s.kumarmeena at sheffield.ac.uk <pchuy1906 at gmail.com>
Mobile: +447470768115
https://scholar.google.com/citations?user=KOz8LOQAAAAJ&hl=en
https://realworldcrystals.leeds.ac.uk/profiles/dr-santosh-kumar-meena/

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


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