GROMACS version: 2023.0
GROMACS modification: No
I was wondering if there is a clear recommendation for the mdp parameters regarding the non-bonded interactions using the AMBER force field?
The GROAMCS manual recommends following parameters when using the CHARMM force field:
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
However, there is no such recommendation in the manual for the AMBER force field.
Doing some research, I came across this post and this post from @alevilla .
In these posts following parameters are recommended for the AMBER force field:
constraints = h-bonds ; bonds involving H are constrained rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) vdw-modifier = Potential-shift-Verlet ; Amber specific DispCorr = EnerPres ; account for cut-off vdW scheme coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics fourierspacing = 0.125 ; grid spacing for FFT
Doing some further research a came across this website that explained how to choose the appropriate cutoff distance. For the AMBER force field, it is 10 Å or 1 nm. The cutoff value depends on the cutoff which was used during the parametrization of the force field. As stated in the primary literature ff99SB, ff14SB, ff19SB and lipids21 were all parameterized using a cutoff value of 10 Å or 1 nm, respectively.
However, reading the primary literature I couldn’t find a reason why
vdw-modifier= Potential-shift DispCorr = EnerPres
are used or why specifically these values are chosen.
I also checked the Sorin Lab website for ffAMBER but I couldn’t find an explanation there.
What is the reasoning for using
vdw-modifier = Potential-shift DispCorr = EnePress
when using the AMBER force field in GROMACS and is there any literature or reference for this available?
Also, if these are the general non-bonded parameters in the mdp file when using the AMBER force field, wouldn’t it be useful to include them in the force field section of the GROMACS manual?
Additinoally, I also use
coulomb-modifier = Potential-shift
when using the AMBER force field. Again in there any literature or reference availbe for this parameter using the AMBER force field?