[gmx-users] PBC correction to visualize a protein-membrane structure

[Justin Lemkul]

On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote:
> Thank you Justin,
>
> please find a dropbox link to the image below.
>
> I’ve used
>
> trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole
> trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center
>
> and different combinations of those
>
> https://www.dropbox.com/s/az1gvb299y6wh8h/Screen%20Shot%202014-05-06%20at%2021.15.07.png
>

Your system was probably centered at z=0 instead of z = z_box/2 (commands used 
for building the system would also help - I guess I should have been more 
clear), hence it's getting split across PBC.  trjconv -trans in conjunction with 
-pbc mol should be what you need.

-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 601
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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