Polarisation group definition

[Michael Schauperl]

Hi all,

I just have another question, which I cannot solve on my own.
I have seen that Polarisation groups are somehow definied in the force field file with the pgrp command. I understood that the number after that command is the atom tpye number.
Anyway no I have the problem that I have a C60 molecule(so all atoms are the same) and i would like to say OpenMM that I want all this atoms in one polarisation group.

Is it sufficient if I use the command:
<Polarize type="401" polarizability="0.00175" thole="0.3900" pgrp1="401" />

Assuming that atom type 401 is my C60 atom typ

Thanks!

Michael

[Peter Eastman]

Hi Michael,

I'm not too familiar with that code, but I'll give it a shot based on my reading of it.

First, are you really sure you want all 60 atoms in the same polarization group? As I understand it, that suppresses certain interactions between them. Do you really want that to happen even for atoms on opposite sides of the molecule? (Maybe you do. I'm just asking.)

Anyway, I don't think the pgrp attributes will actually do that. As far as I can tell, it still only looks at 1-2, 1-3, and 1-4 bonded pairs. The pgrp attributes specify atom types that, if they appear among those closely bonded atoms, should be considered to be in the same polarization group.

But I might be misunderstanding all of it. Like I said, I'm not that familiar with it. The code in question is the setPolarGroups() function in forcefield.py. Take a look and see if it makes sense to you.

Peter

[Michael Schauperl]

Hi Peter,

Thanks for the answer. I see now where the problem is. The polarisation groups seems to overlay and probably this is not working. I changed my definition now that every atom is a own polarization group. This works!

Thanks for your help!

Michael