[gmx-users] Mass in GMX topology

Justin Lemkul jalemkul at vt.edu
Thu Jul 11 14:27:16 CEST 2013



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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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