[gmx-users] Frozen atoms and energy group exclusion

[Mark Abraham]

>      When I run this through grompp, I get the following error:
> WARNING 1 [file "dppc.top", line 19]:
>   Can not exclude the lattice Coulomb energy between energy groups
> Checking consistency between energy and charge groups...
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: grompp.c, line: 307
>
> Fatal error:
> atoms 3212 and 3213 in charge group 2179 are in different energy groups
> -------------------------------------------------------
>
> Am I doing this incorrectly?  Should I be excluding the interactions with
> the
> frozen groups in another way?

Have a look at the description of charge groups in 4.6.2 and 4.6.3 and the
implementation of this in 5.5.1. grompp is evidently complaining that your
charge group boundaries are not the same as the energy group boundaries,
and since non-bonded energies are calculated looping over charge groups,
this is a fine thing for it to be unhappy about! So have a look at the
charge groups in your DPPC molecule and see if you can come up with a
compromise that keeps charge group neutrality.

Mark