[gmx-users] Significance of box vectors in GRO trajectory file.

[Justin Lemkul]

On 6/5/17 10:14 AM, Dawid das wrote:
> By "rewraping coordinates" do you mean how molecules that went outside of
> the box are treated?
> 

I mean you're changing the distance between periodic images after the 
simulation, which means whatever reimaging you are doing via trjconv is wrong 
relative to what actually happened during the simulation.

> By the way, why does this vector change during simulation? What if I use
> exactly the same vector for my whole
> simulation?
> 

This is the function of pressure coupling.  If you keep the box vectors fixed, 
that is an NVT simulation.

-Justin

-- 
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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
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Baltimore, MD 21201

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

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