[gmx-users] Genbox command question

Fabian Casteblanco fabian.casteblanco at gmail.com
Fri Apr 15 21:33:59 CEST 2011


I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
parameters in a -box 6 6 6.   After minimization, I realized that for
a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
be exact, with electrostatic coloumb potential the greatest
contributor.  I used the same thing with OPLSA FF parameters and got a
'+3 kJ/mol'.  I realize that when I place 1000 of these molecules, the
potential will be very high since the potentials are positive to begin
with.  When I placed 1000 molecules using:

-     "genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro"

I resulted with a box full of 1000 molecules in that specific box size
on gromacs 4.0.1.  I did the same on the latest gromacs 4.5 but it
ended up taking longer and the last line stating 'killed'.  I redid it
with a box 7 7 7 and it worked on gromacs 4.5.   However, after I
energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and
(box 7 7 7 on gromacs 4.5), the first gave me a large negative
potential energy (-6000 kJ/mol) after taking a long time and the
second box gave me a somewhat large 2*10^3 kJ/mol.  I am still new to
Gromacs but I'm confused on why a certain box size worked on one
version of gromacs and the other didnt.  I assume that the difference
in potential energies is since the 2nd box has way more space for
these molecules therefore they are not as well equilibrated as the
more compact box of size 6 6 6.  Why does my box size that worked on
gromacs4.0.1 work and on 4.5 it states killed as the last line and
only works redoing it with a bigger box size.

Thank you so much for your time and help ahead of time.

Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com

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