Adjustment in the mdp files for CHARMM36m

GROMACS version:2020
GROMACS modification: Yes/No
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I want to use the CHARMM36m forcefield. This website said

For using CHARMM36 in GROMACS 5.0 and newer, please use the following settings in the mdp file:

constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

I am following Justin’s lysozyme tutorial, in which the mdp files include

My questions are

  1. The so-called “use the following settings in the mdp” only refers to the md.mdp file?

  2. The Justin’s tutorial uses the OPLS forcefield. To adapt to the CHARMM36m FF, should I simply copy those lines (i.e. constraints = h-bonds, cutoff-scheme, etc.) at the end of his mdp file, so that those parameters will be overwritten?

No, everything needs to be done consistently and using the proper settings for the force field, except ions.mdp, which is not used for a simulation so its contents are irrelevant.

grompp will complain about double entries for keywords. Replace the values with proper ones.

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Hello Justin,
Thanks for your feed,. My question might be … I searched in many publications still have doubts. I have only protein in two separate chains for Gromacs MD simulation with CHARMM36m. What is the best strategy for tcouple and pcouple? I really appreciate your guide here for. Dylan

What do you mean? Algorithms? Assigning tc-grps?

Thank you. I mean the thermostat and barostat in the mdp files? . The algorithms

Anything except the Berendsen weak coupling method is valid. Studies should specifically state what was used in publications.

Dear Dr. Lemkul, thank you so much. Well understood.