[gmx-users] Regarding-virtual-sites-tutorial

[Justin Lemkul]

On 8/1/15 7:08 PM, sujithkakkat . wrote:
> Dear Justin,
>
> I am following your tutorial about CO2 topology using virtual sites.
>
> I find that in the topology provided, you have not reassigned the particle
> type as virtual (V) for the C and O atoms (which are treated as the virtual
> sites in the model). Instead, they are directly selected from the OPLSAA
> forcefield files, in which the particle type is always 'A'.
>
> I was wondering if the choice of particle type has any effect on the
> results.
> Please comment.
>

No idea. I never checked to see whether the CO2 model is physically sensible at 
all (and I do warn about this fact in the tutorial).  It's just a very simple 
demonstration of how to calculate constructing constants and the math behind the 
moment of inertia stuff, since for a while it was a common question on the 
mailing list.

-Justin

-- 
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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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