[gmx-users] moved atoms

Justin Lemkul jalemkul at vt.edu
Wed Oct 21 03:49:54 CEST 2015

On 10/20/15 7:05 PM, Sana Saeed wrote:
> good morning gmx users!i am simulating a Prion Protein (Residues:104) after
> NPT some of the atoms move out of the box, and the values of box vectors are
> also decreased, and when i add the highest value of the x coordinate with 1,
> it doesn't give me the value of vector.

There is no "outside" of a periodic unit cell.  If the visualization is 
inconvenient for you, that's what trjconv is for.

Box vectors will vary during NPT as the density equilibrates, so this is expected.



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


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