Hi Justin and all,
Using Morse = yes for the anharmonic potential option, whereas using the parameters below for the hard wall restraint option?> > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamics simulations of the > > graphene-water interface > > > > Of course you can implement whatever you like. Gromacs has been able to carry > out polarizable simulations for a very long time; I've only ever cautioned > against abuse of certain models. > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > polarisable calcs, they are prone to polarisation catastrophe due to the > massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint.
pbc = xy
nwall = 2
wall-atomtype = ; optional
wall-type = 12-6
wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run
wall-density = 5 5
wall-ewald-zfac = 3
> In the paper mentioned above, the authors have carried out three types of cals: > i) SPC/E on non-pol graphene > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > charge): graphene-DP in neutral or charged states > > They seemed to have simulated their systems using both additive and polarisable > (0.878 angstrom^3) models? > I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes.
Yep, now I understand it.
If I wanted to also describe graphene, is it possible to include carbon parameters in the SWM4-NDP force field then?
You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30?> > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > instead of shelltype particle). > > > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > can it be replaced with an atom (assuming an induced dipole model) instead of > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > opposite charge of the water oxygen atom? > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > atoms. There's nothing conceptually special about them, we just handle them > slightly differently in the code. > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > to experiment if I can: > i) replace the Drudes to atom with the same configuration - opposite charge, > mass (0.4 amu), lengths, etc > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried out differently, so no, this sort of hacked approach probably isn't very robust.
As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right?
To relax a system containing Drude particles, is md=steep enough, or the more accurate conjugate gradient?
I get unreasonable energy minimised confout.gro structure very often, if there are Drude-based ions included (head-scratching).
> OR > > ii) switch to the more stable SWM4-DP with the hydronium and hydroxide > implementation from David van der Spoel? I don't know how this relates to the point above about graphene, so I'm a bit lost. SWM4-NDP is a better model than SWM4-DP, FWIW.
Absolutely, no doubt about that; SWM4-NDP describes water surf.tension better than SWM4-DP.
It was just a thought, that if SWM4-NDP becomes very unstable upon the inclusion of polarisable ions (e.g. hydronium and hydroxide that also contain Drude particle), SWM4-DP could be an alternative?
Using Morse = yes for the anharmonic potential option, whereas using the parameters below for hard wall restraint?> > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamics simulations of the > > graphene-water interface > > > > Of course you can implement whatever you like. Gromacs has been able to carry > out polarizable simulations for a very long time; I've only ever cautioned > against abuse of certain models. > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > polarisable calcs, they are prone to polarisation catastrophe due to the > massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint.
pbc = xy
nwall = 2
wall-atomtype = ; optional
wall-type = 12-6
wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run
wall-density = 5 5
wall-ewald-zfac = 3
> In the paper mentioned above, the authors have carried out three types of cals: > i) SPC/E on non-pol graphene > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > charge): graphene-DP in neutral or charged states > > They seemed to have simulated their systems using both additive and polarisable > (0.878 angstrom^3) models? > I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes.
Yep, now I understand it.
Is it possible to include the carbon parameters in the SWM4-NDP force field to describe/represent graphene?
You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30?> > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > instead of shelltype particle). > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > can it be replaced with an atom (assuming an induced dipole model) instead of > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > opposite charge of the water oxygen atom? > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > atoms. There's nothing conceptually special about them, we just handle them > slightly differently in the code. > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > to experiment if I can: > i) replace the Drudes to atom with the same configuration - opposite charge, > mass (0.4 amu), lengths, etc > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried out differently, so no, this sort of hacked approach probably isn't very robust.
As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right?
> OR > > ii) switch to the more stable SWM4-DP with the hydronium and hydroxide > implementation from David van der Spoel? I don't know how this relates to the point above about graphene, so I'm a bit lost. SWM4-NDP is a better model than SWM4-DP, FWIW.
Absolutely, no doubt about that; SWM4-NDP describes water surf.tension better than SWM4-DP.
It was just a thought, that if SWM4-NDP becomes very unstable upon the inclusion of polarisable ions (e.g. hydronium and hydroxide that also contain Drude particle), SWM4-DP could be an alternative?
Thanks again for the information, really appreciate it.
Regards,
Kester
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