[gmx-users] Virtual sites and diffusion coefficients.

[Justin Lemkul]

On 2/3/15 3:56 AM, sujithkakkat . wrote:
> Hello Mark,
>
>       I have tested both models in simulating a variety of properties. The
> original parametrization results involved predicting the critical point of
> CO2 and also density at various P and T. I did several NVT simulations to
> predict density-vs-pressure data. In this case the model with virtual
> interaction sites gave much better results.
>
>       In addition to this, simulations performed were performed on pure CO2
> at supercritical conditions and mean square displacement was calculated for
> the CO2 molecule. When compared to the reported ab initio dynamics results
> the one obtained  using virtual sites gave much better agreement.
>
>       The density of CO2 dissolved in H2O at very dilute concentrations was
> also studied using both models of CO2 and the results were in good
> agreement with experimental data for the model with virtual sites. In this
> case the one without virtual sites also did reasonably well.
>
>        However, the disparity appears when considering the Measn Square
> displacement of dilute CO2 solution in water. Here the model without
> virtual sites is closer to the experimental data.
>
>      This has become very confusing now. The original parametrization of he
> model did not involve predicting the transport properties. Also in the
> published results using the EPM2 model  I don't find any mention of the
> virtual interaction sites.
>

I'm rather amazed that my tutorial model works so well, but please note the 
strong caution I wrote in the topology.  There is no validation of this model at 
all, anywhere in the literature.  Any reviewer of your work is going to 
certainly want an explanation of the parameters, and "some model from a tutorial 
that says it isn't guaranteed to be physically valid" probably isn't going to 
satisfy them.

-Justin

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

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
http://mackerell.umaryland.edu/~jalemkul

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