[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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