[gmx-users] CHARMM36 and energygroup exclusions

[Daniel Bauer]

On 05/02/2017 07:45 PM, Justin Lemkul wrote:
>
> Your input configurations is probably broken across PBC, so grompp
> does a clunky calculation and thinks things are split really far
> apart.  It doesn't matter though, because CHARMM36 doesn't use charge
> groups.  Every atom is its own group so by definition you can't have
> any problems with this.
>
> -Justin 

This is very likely the case since the input structure is the output
.gro from a previous run equilibration simulation. I think I was
irritated because http://www.gromacs.org/Documentation/Errors suggests
that for broken molecules "the sum of the two largest charge groups will
correspond to a value twice the box vector along which the molecule is
broken". However, the sum is not exactly twice my box length in x,y or
z. Thinking about it, I guess the vector must not neccessary be in the
direction of one axis though.

Just to be sure, do you think these settings are fine for the given
scenario?

Thanks,
Daniel