Dear Gromacs users,
I am trying to perform a simulation for a protein-DNA system using GROMACS 2019. I would like to use both CHARMM22 and AMBER99SB-ILDN force fields for force field comparison.
non-bonded settings for AMBER99SB-ILDN:
coulombtype = pme
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
pme_order = 4
fourierspacing = 0.16
non-bonded settings for CHARMM22:
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
pme_order = 4
fourierspacing = 0.16
During production run tpr file generation (using grompp), I saw the following messages:
using CHARMM22 force field:
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
using AMBER99SB-ILDN force field:
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Significantly very few non-bonded parameter combinations were generated during grompp, using AMBER99SB-ILDN force field compared to CHARMM22. I am confused regarding this issue.
Any kind of advice/ suggestions will be deeply appreciated.
Thanks in advance,
Snehasis Chatterjee