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

[Justin Lemkul]

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 
potential.

> 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 
anharm_polarize().

> 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?
>

Yes.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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