[gmx-users] centering a protofibril in a box

Justin Lemkul jalemkul at vt.edu
Thu Nov 6 13:54:19 CET 2014

On 11/6/14 6:13 AM, Adriana Garro wrote:
> Dear all,
> I am trying to center a protofibril in a box, but respect to its first
> monomer. (the result would be the protofibril shiftted to the botton of the
> box)
> I used
> trjconv -f protofibril.pdb -n index.ndx -center -s  protofibril.pdb -o
> test.pdb
> I did an index for the residues corresponding to the first monomer and that
> is which I chose as "select group for centering" but when I visualize the
> System with vmd the protofibril appears in the center of the box but as it
> was just one molecule.

You can accomplish this with either editconf -translate or trjconv -trans.  I 
don't exactly know what's going on from your description - an image here would 
be good, because the last sentence doesn't make much sense to me.



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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