[gmx-users] Problem with constraints in NVT calculations.
jalemkul at vt.edu
Tue Oct 14 14:00:45 CEST 2014
On 10/14/14 7:40 AM, Kester Wong wrote:
> Hi Justin and all,
> > > > 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.
> > Using Morse = yes for the anharmonic potential option, whereas using the
> > parameters below for the hard wall restraint option?
> > 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
> No. I'm not suggesting a Morse potential. What I was referring to was an
> anharmonic function for the bonds, which is present in Gromacs but I'm not sure
> if it's documented. The wall settings in Gromacs have nothing to do with this.
> Such a function is not present in Gromacs (yet).
> Although the wall settings have nothing to do with polarisation catastrophe, I
> guess it might be useful in the following case:
> I have been using a time step of 1 fs, which is small already, yet the water
> droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the
> z-direction. I will try using the wall setup as above, hoping that water remains
> a droplet with the presence of H3O and Cl ions. Could you please explain what is
> the difference between the three types of wall; 9-3, 10-4, and 12-6?
The exponents used in the LJ potential for the wall. 12-6 is the "normal" LJ
> The only part of the GROMACS 5.0 manual that described anharmonic bond potential
> is in the Morse potential section 4.2.2.
Like I said, it's not documented. See src/gromacs/gmxlib.c, function
> Which function is not available in GROMACS yet?
What we call the "hard wall" restraint, that reflects a Drude particle along the
bond vector connecting it to its parent atom. It prevents the Drude from moving
more than a specified amount, thus vastly improving integration stability. See
the Appendix of dx.doi.org/10.1021/jp402860e.
> > > 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?
> Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force
> field, you're creating a force field that describes both. This can certainly be
> done if you have all the parameters.
> That is great! To create a FF that describes the SWM4 water, NDP ions, and
> graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded
> parameters, and the LJ nonbonding interaction parameters, is that right?
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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