[gmx-users] Potential energy

[Justin Lemkul]

On 2/21/16 3:35 PM, mohammad r wrote:
> Thank you Justin,
>
> do you know how I can find or modify the center of mass velocity of my system?
>

During the run?  If using comm-grps (you should for any system with PBC), then 
the COM velocity should be kept at or close to zero.  You can confirm after the 
run with gmx traj -ov -com and select "System."

-Justin

>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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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

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