[gmx-users] Protein goes out of the box

[Justin Lemkul]

On 4/25/17 10:35 AM, spss4 at iacs.res.in wrote:
> Hii all,
> I have simulated protein in 45% ethanol water mixture for 100ns. After
> completion of the job I saw that maximum portion of my protein goes out of
> the box. Then I have done trjconv -pbc mol to the trajectory file. After
> trjconv some portion of the protein is still out of the box. I want to see
> the local environment of the protein using the .gro file(last frame) but
> some portion of protein is dry. How can I get the actual state of protein
> after completion of 100ns?

You may need a few iterations of trjconv to get what you want.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-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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