[gmx-users] Problem with constraints in NVT calculations.

Justin Lemkul jalemkul at vt.edu
Wed Oct 8 23:16:20 CEST 2014

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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