[gmx-users] Using CHARMM36 in GROMACS
gpoon at gsu.edu
Wed Mar 30 23:18:10 CEST 2016
I am learning how to perform dynamics on double-stranded DNA sequences
using the CHARMM36 FF I downloaded from the MacKerell lab. I have
consulted the GROMACS documentation page regarding specific settings in
the .mdp file for CHARMM36
and adopted those for the energy minimization step. In these settings,
constraints = h-bonds. My question is: for the subsequent equilibration
steps, I have read that one should use constraints = all-bonds, but I
have also read that might adversely affect 1-4 interactions. And what
about DispCorr: should I keep = none or one of the other options -- or
does it matter?
Thank you in advance. If there is some other resource that gives all
the FF-specific settings, I would love to know about it.
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