[gmx-users] Using CHARMM36 in GROMACS

Gregory Poon gpoon at gsu.edu
Wed Mar 30 23:18:10 CEST 2016

Hello everyone,

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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