[gmx-users] CHARMM36 GROMACS implementation
jalemkul at vt.edu
Tue Nov 20 00:48:02 CET 2018
On 11/19/18 11:32 AM, John Whittaker wrote:
> Hi all,
> I am trying to reproduce the pure DPPC bilayer data found in J. Chem.
> Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using
> the recommended protocol given in the paper.
> Recently, I realized I made a mistake and have been using the CHARMM36
> forcefield provided by Tom Piggot here
> rather than the official CHARMM36 implementation found on the MacKerell
> lab's site (http://mackerell.umaryland.edu/charmm_ff.shtml).
> From what I understand from its description in the force field
> documentation and the accompanying paper, the version provided by Tom
> Piggot should not affect my results because the lipid parameters from
> CHARMM36 are unchanged (while the protein parameters are) and my system
> consists only of water and DPPC.
> Am I right to assume that my results should be (theoretically) reflective
> of those that I would obtain from using the using the full CHARMM36 force
The lipids should all be the same. A single-point energy/force
evaluation under both force fields would confirm this.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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