Hello GROMACS Users,
I was wondering if anyone who has experience with simulations using
polarization would be willing to take a look at what I’ve tried that so far
hasn’t worked and give some tips and perhaps share their topology files and run
settings. I am attempting to model a 3-atom molecule with polarizability of the
partial charge on each atom. The only examples I have found so far through the
other posts have been for Justin Lemkul’s DrudeFF branch, but I was hoping to
just use the regular release if that is possible.
I have included my .itp files for things I have tried that have not worked-
Version 1, no explicitly defined shell particles – made with the assumption
that Gromacs would handle generating the shell particles for me given the host
and a polarizability.
[ moleculetype ]
; molname nrexcl
ozone 2
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OzCs94e8 1 OZO OzC 1 0.3 15.9994
2 OzSs94e8 1 OZO OzS1 1 -0.15 15.9994
3 OzSs94e8 1 OZO OzS2 1 -0.15 15.9994
[ bonds ]
; i j funct length force.c.
1 2 1 0.1278 182000
1 3 1 0.1278 182000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 116.8 587.7
[ polarization ]
; atom i j type alpha
1 2 1 0.00095
2 3 1 0.00095
3 1 1 0.00095
Version 2, explicitly assigned shell particles (shell atoms defined as shell
type in the ffnonbonded.itp file)
[ atomtypes ]
OzCs94e8 8 15.9994 1.30 A 3.02e-01 5.2216e-01
OzSs94e8 8 15.9994 0.85 A 3.02e-01 5.2216e-01
OzCs94e8s 8 0 -1 S 0
0
OzSs94e8s 8 0 -1 S 0
0
[ moleculetype ]
; molname nrexcl
ozone 2
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OzCs94e8 1 OZO OzC 1 1.3 15.9994
2 OzCs94e8s 1 OZO OzCs 1 -1 0
3 OzSs94e8 1 OZO OzS1 1 0.85 15.9994
4 OzSs94e8s 1 OZO OzS1s 1 -1 0
5 OzSs94e8 1 OZO OzS2 1 0.85 15.9994
6 OzSs94e8s 1 OZO OzS2s 1 -1 0
[ bonds ]
; i j funct length force.c.
1 2 1 0.1278 182000
1 3 1 0.1278 182000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 116.8 587.7
[ polarization ]
; atom i j type alpha
1 2 1 0.00095
3 4 1 0.00095
5 6 1 0.00095
Thanks,
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