Mdp parameters for non-bonded interaction using the AMBER force field

Hi Eddie,

maybe this helps you (from the AMBER22 manual):

In the section: 21.7.2. Particle Mesh Ewald

The Particle Mesh Ewald (PME) method is always on … Please take care in changing any values from their defaults."

Then further down in the section describing the options of PME:

vdwmeth: Determines the method used for van der Waals interactions beyond those included in the direct sum. A value of 0 includes no correction; the default value of 1 uses a continuum model correction for energy and pressure.

We can probably assume this is equivalent to gmx DispCorr.

Further in: 21.7. Potential function parameters

fswitch: When off, fswitch<=0 , uses a truncation cutoff. When on fswitch>0, sets a force switching region where the force cutoff smoothly approaches 0 between the region of the fswitch value to the cut value. Force values below the fswitch value follow the standard Lennard-Jones force. Default is -1. This option is not supported for use with GB (i.e., only igb=0 and ntb>0), nor is it compatible with the 12-6-4 Lennard-Jones model (lj1264=1). Due to performance regressions (about 20%) with running with the force switching on, it is recommended that simulations run with fswitch off unless using a force field that requires or recommends using the force switch.

Therefore, the only gmx vdw-modifier that fits the current default behavior of AMBER:

vdw-modifier = Potential-shift
DispCorr = EnerPress

These are more general recommendations and not really force field specific. However, I guess we are looking for a reference one can cite that explicitly states this. There are references scattered in this section of the AMBER manual and one might find something there.

And just to make sure we are on the same page, the ff14sb publication also implies (again, please correct me if I am wrong):

rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm)

What makes all of this confusing to me is that there are publications out there (at least one) that use GROMACS in combination with the ff14sb forcefield without stating the specific options used.

Still, until ff14sb is officially supported with recommended parameters we probably should no be working with it if we want to publish. As far as I know, the GROMACS devs have stated that this depends on a validation that should be performed by the users once, which is understandable given that GROMACS is free and open source (which is great!). However, that this has not happened yet is astonishing. Are there any test systems/protocols in place that might constitute a proof? Interestingly, some work in this direction on a modified version for RNA/DNA simulations of ff14sb is done here.

I welcome any corrections if something I said is inaccurate.