[gmx-users] editonf: Center of Mass?

Nicola Staffolani n.staffolani at unitus.it
Fri May 30 12:05:15 CEST 2014

Dear gmx community,

I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
when I create the box and put H2O molecules inside using editconf, since
the planar dimensions of the Au layer are big compared to the corresponding
dimensions of the molecule, I have decided that I want my box to be

After that I give the box vector lengths a,b and c, I get that along the
direction perpendicular to the Au layer the box is shifted with respect to
the system (= Au layer + molecule). In order then to fully enclose the
system with H2O molecules, what I did is to make the box bigger, but this
costs time and I would like to understand what is happening and find a
proper solution.

I have read the gmx online reference about editconf
<http://manual.gromacs.org/online/editconf.html>: where it is said that
"Both -box and -d will center the system in the box", is the Center of Mass
(CoM) meant?? This would make sense, since my shifted box is shifted
towards the Au layers, whose Au atoms are much heavier than the atoms of
the molecule. What I would like to achieve is to geometrically (and not
gravitationally) center the system inside my box, getting rid in this way
of the H2O molecules which are under the Au layers. Is there any smarter
way to use editconf to achieve that without resorting to manually
eliminating the unwanted H2O molecules?

​For completeness of information, my executable water.com ​
​file is:

editconf -f speptide.gro -o -bt triclinic -box 7.2 5.4 6.4
genbox -cp out -cs   -p speptide -o speptideh
editconf -f speptideh     -o azwater.pdb

Thank you in advance,

Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36

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