openmm
Using Amoeba implicit solvent: can we specify salt concentration by Debye-Huckel screening parameter(`implicitSolventKappa`)?
Hello,
I was trying to use the amoeba2018 force field and amoeba2018_gk implicit solvent model but wondering if I could specify salt concentration in the same way as I did to Amber implicit solvent models by Debye-Huckel screening parameter (docs link). So I tried to add implicitSolventKappa argument to forcefield.createSystem() like this:
forcefield = ForceField('amoeba2018.xml', 'amoeba2018_gk.xml')
system=forcefield.createSystem(self.topology, nonbondedMethod=NoCutoff, implicitSolventKappa=2.0/nanometer, soluteDielectric=1.0, solventDielectric=78.5)
but I got an error as follows:
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/cuda11.4/openmpi4/openmm/7.7.0/lib/python3.8/site-packages/openmm/app/forcefield.py", line 1377, in createSystem
args.checkArgs(self.createSystem)
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/cuda11.4/openmpi4/openmm/7.7.0/lib/python3.8/site-packages/openmm/app/internal/argtracker.py", line 24, in checkArgs
raise ValueError(f"The argument '{key}' was specified to {fn.__name__}() but was never used.")
ValueError: The argument 'implicitSolventKappa' was specified to createSystem() but was never used.
I also tried another argument implicitSolventSaltConc and got the same value error.
According to the documentation (http://docs.openmm.org/latest/userguide/application/02_running_sims.html#implicit-solvent-and-solute-dielectrics), it looks like Amoeba implicit solvent models (amoeba2018_gk or amoeba2009_gk) only allow users to modify dielectrics of solvent and solute - is there any way to modify salt concentration? If not, what is the default salt concentration?
Thank you very much!
Amoeba GK doesn't try to model salt. I believe it's equivalent to pure water with no salt.
Thank you for the clarification! It makes sense now - All of the Amber implicit solvent models in OpenMM are Generalized Born models, instead of Generalized Kirkwood.
In the paper refered to by amoeba2018_gk.xml, it writes:
Throughout the current work we neglect salt effects, although their addition to a future GK formulation is straightforward. (Michael J. Schnieders and Jay W. Ponder. J. Chem. Theory Comput. 2007, 3, 6, 2083–2097)
I'm testing Amoeba2018 + Amber GB implicit solvent models. Thanks again!
I'm testing Amoeba2018 + Amber GB implicit solvent models.
You can try that, but I'm doubtful it will work. GB models are designed to exactly cancel a fraction of the Coulomb interaction, where the fraction depends on distance and on the Born radius. AMOEBA has a different functional form for the Coulomb interaction that involves the multipole moments. That means GB won't cancel it out in the way it's supposed to.
Perhaps @mjschnie can comment on how hard it would be to generalize the GK model to support salt.
You can try that, but I'm doubtful it will work. GB models are designed to exactly cancel a fraction of the Coulomb interaction, where the fraction depends on distance and on the Born radius. AMOEBA has a different functional form for the Coulomb interaction that involves the multipole moments. That means GB won't cancel it out in the way it's supposed to.
That makes a lot of sense. I think I probably will eventually go back to use Amber forcefield and Amber implicit solvent.