Adjustment in the mdp files for CHARMM36m

User discussions
1

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
ions.mdp
minim.mdp
nvt.mdp
npt.mdp
md.mdp

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?

2

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.

1 Like
3

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

4

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

6

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

7

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

8

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