[gmx-users] CHARMM36 and energygroup exclusions

Justin Lemkul jalemkul at vt.edu
Wed May 3 14:07:15 CEST 2017

On 5/2/17 6:17 PM, Daniel Bauer wrote:
> 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?




Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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