[gmx-users] Potential energy

[mohammad r]

Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system? 

    On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 

 

On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
>

As a broad generalization, but strictly speaking, that's not always true.  A 
comparable protein in a similarly sized box will probably have something on that 
order, but that is by no means an absolute rule.

-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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