[gmx-users] CHARMM36 and energygroup exclusions

Daniel Bauer bauer at cbs.tu-darmstadt.de
Wed May 3 00:17:13 CEST 2017

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


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