[gmx-users] center of box protein

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 2 16:37:57 CEST 2011

nahren manuel wrote:
> Dear GMX users,
> I am trying to center my protein at the center of box using editconf. 
> When I view the same using ngmx, the protein seems to lie outside the box
> neweditconf -f alapdb.pdb -bt cubic  -o boxpdb.pdb -c -center -0.156 
> -0.061 0.084 -d 1.5

The protein appears "outside" of the box (which is irrelevant in a periodic 
system, anyway) because you're putting it there.  You've specified negative 
coordinates.  Gromacs builds all boxes from the coordinate origin into the 
quadrant where (x,y,z) are all positive.

> this one works, but the molecule is shifted.
> neweditconf -f alapdb.pdb -bt cubic -d 1.5 -o try.pdb
> I want my molecule (geometrical )  center to be the center of the box 
> with -d 1.5.

Just use editconf -c -d 1.5; I don't know what "shifted" means above, because 
the combination of -c and -d should center the protein in the box (in fact, the 
use of -d automatically triggers -c).  Using -center overrides it with whatever 
you specify and is only necessary for custom placement.


> Best,
> nahren


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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