On 10/8/14 8:57 AM, Kester Wong wrote:
Hi Justin,
> 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.
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.
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.
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.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
