[gmx-users] Genbox command question

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 15 21:45:42 CEST 2011

Fabian Casteblanco wrote:
> Hello,
> 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:

This is not necessarily true.  Isolated molecules can have positive potential 
energies due to unsatisfied interactions, but in a condensed phase, the presence 
of other molecules produces negative energies due to favorable van der Waals and 
hydrogen bonding interactions.

> -     "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

Simulations with version 4.0.1 will be extremely slow due to a critical bug that 
was introduced.  You should not use version 4.0.1; it was removed from the 
website within hours of its release due to series performance problems.

> second box gave me a somewhat large 2*10^3 kJ/mol.  I am still new to

A more expanded system will have unsatisfied interactions, thus positive energy.

> 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

That's hard to pinpoint.  If you have a 7-nm cubic box, gentle equilibration 
should produce a reasonable density and a much lower potential.

> 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

Energy minimization and equilibration dynamics are different.  A more dense 
system is simply more favorable.  You can certainly achieve an equivalent result 
with proper NPT equilibration.


> 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


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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