[gmx-users] editonf: Center of Mass?

Justin Lemkul jalemkul at vt.edu
Fri May 30 14:30:44 CEST 2014

On 5/30/14, 6:32 AM, Nicola Staffolani wrote:
> 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
> triclinic.
> 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?

You can define whatever position you like with -center based on whatever box 
size is appropriate, rather than relying on -box and/or -d, if they are giving 
undesirable results.


> ​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​


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


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