[gmx-users] Mass in GMX topology

[Justin Lemkul]

On 7/11/13 8:17 AM, Steven Neumann wrote:
> Thank you. Another question: Does RDF depends on the mass of the atom? On
> the one hand it gives different value of the force in equation of motion
> but on the other hand velocities are rescaled with a thermostat.
>

My impression would be that the masses always affect the dynamics, but in this 
specific instance, I can't say how the outcome will change.  I think it would 
also depend on the magnitude of change in the mass and whether or not you can 
sample enough to ever see a difference because of it.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

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