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

Justin Lemkul jalemkul at vt.edu
Wed Oct 8 13:31:57 CEST 2014

On 10/7/14 10:59 PM, Kester Wong wrote:
> Hi Justin,
> Thank you for the clarification. I should look into using NAMD.
> The new polarisable Drude implementation will surely benefit everyone in the MD
> community.
> I am looking forward to using it, as with others (I think there was a similar
> post by Yana Tsoneva on this issue too, dated back in July).
> 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.

> 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.



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


More information about the gromacs.org_gmx-users mailing list