[gmx-users] Dummy atom vs Real atom

[Justin Lemkul]

On 7/21/17 11:30 AM, Mostafa Javaheri wrote:
> Dear gmx users
> 
> Does anyone know how a dummy atom with no Van der Waals interactions
> (zero sigma and epsilon parameters) and also no mass and charges deals
> with other real atoms inside the simulation box? Is that possible a
> dummy atom with described characteristics get infinitely close to a
> real atom during the simulation? Or even passing through each others?

"Dummy" atom may refer to a couple of different cases, but as you describe, a 
non-interacting species would indeed just diffuse through the box and not 
interact with anything (including overlap).

-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

==================================================