[gmx-users] Regarding minimum protein-edge distance and dispersion correction for Charmm27 (Charmm22/CMAP) or Charmm36 FF
jalemkul at vt.edu
Wed Sep 28 15:50:21 CEST 2016
On 9/28/16 5:45 AM, Rakesh Ramachandran wrote:
> Dear Gromacs users,
> I am using Charmm36 FF with Gromacs 5.1 GPU version for running my
> protein simulations. With respect to the minimum protein-edge distance for
> Charmm FF I see in the literature that it should be greater than 1.2nm, as
> rcoulomb value is 1.2nm and also for proper screening of electrostatic
> interactions between copies of the protein across periodic boundaries.
> 1) My question is can a minimum protein-edge distance of 1.0nm be used
> in the protein MD simulations (I see this value in a lot of publications)
> and has anyone encountered problems in electrostatic energy values for the
> Charmm FF because of using 1.0nm cutoff.
I would consider a 1.0-nm solute-box distance a bare minimum. It will satisfy
the minimum image convention unless the box size changes drastically.
> 2) Moreover should dispersion correction be enabled by setting DispCorr
> value to Yes for Charmm FF for protein MD simulations.
> 3) Which is the current release which would be ideal to use with Charmm
> FF - Gromacs 5.1.4 or Gromacs 2016 ?
Use of the force field is not version-dependent.
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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