[gmx-users] editconf - CoM?

[Nicola Staffolani]

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?

​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​

-- 
​​
"New ideas, fragile as spring flowers, easily bruised by the tread of the
multitude, may yet be cherished by the solitary wanderer.", Fred Hoyle, *The
Black Cloud*.

"Everybody knows that something can't be done until somebody turns up who
doesn't know that it can't be done and he does it.", Albert Einstein

Sometime ago I met a fellow who was wearing an abnormally long tie - I
mean, it was abnormally long because of how the knot had been made, not
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his grandfather!!