[gmx-users] Fwd: Peptide out of box even after applying trjconv

[Justin Lemkul]

On 6/14/17 6:27 AM, Apramita Chand wrote:
> Dear All,
>   Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact
> -center -o newfile.gro,
> for visualisation purposes of peptide inside the box, a portion of it still
> sticks out of the box. Is it unnatural?
> 
> What might be done to sort out the problem?
> 

There's no such thing as "outside" a periodic system.  Depending on your box 
size, things may protrude from the central image but it's not necessarily wrong. 
  What you should ensure is that your box is large enough to avoid minimum image 
violations.  gmx mindist -pi is useful here.

-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
20 Penn St.
Baltimore, MD 21201

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

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