[gmx-users] Inorganic Material Simulations

Justin Lemkul jalemkul at vt.edu
Wed Aug 5 01:25:15 CEST 2015

On 8/4/15 6:58 PM, ANAND AMITKUMAR Dharia wrote:
> Hey there,
> I am interested in simulating a protein diffusing inside an inorganic
> nanotube. I want to study how the diffusivity of the protein changes as a
> results of the surface interaction with the nanotube. Specifically, I am
> looking to understand how to define a force field for the nanotube and
> protein/solvent interactions. Additionally, I want to know if I can
> restrain the atoms of the nanotubes only and use these atoms solely for
> polarizable effects within the simulation space. I have looked into the
> drude oscillator force field and am trying to understand how I can
> implement this model. Please let me know any advice or point me to some
> documentation of how I can approach this.

The Drude model is already implemented.  The problem is there is no support for 
inorganic nanotubes in the force field (we have proteins, carbohydrates, DNA, 
water, ions, a limited set of other things).  Deriving suitable force field 
parameters for something like that is a Ph.D. project in itself.



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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