[gmx-users] Regarding minimum protein-edge distance and dispersion correction for Charmm27 (Charmm22/CMAP) or Charmm36 FF
korenpol3 at gmail.com
Wed Sep 28 11:45:42 CEST 2016
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.
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 ?
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