[gmx-users] fixing PBC view

Justin Lemkul jalemkul at vt.edu
Sun Feb 7 20:14:46 CET 2016

On 2/7/16 7:48 AM, Netaly Khazanov wrote:
> Hi All,
> My system is including the small compound with penetrates the membrane
> lipids. I've ran the MD simulation and now trying to get rid off the PBC
> view and create a nice movie. The problem that I've managed to fix PBC view
> of the lipids, however the location of small compound still indicates the
> wrong position related to membrane. Any ideas how to fix it will be
> appreciated.
> The command that I used:
>   trjconv_d -s md.tpr -f md.xtc -o md_noPBC.pdb -pbc mol -center -n -ur
> compact # centering on POPC group
> I've used the numerous variation  but none does work.

Most likely you need to fit the small molecule's position with, e.g. -fit 
transxy after the above centering command.



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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