[gmx-users] Polarization assistance request

[Heroneme, Carl Joseph]

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,