[gmx-users] Re: Genbox command question

[Fabian Casteblanco]

Thank you Justin.

Your explanation really helped.  I was actually using 4.0.5, not 4.0.1
(my mistake).  Your explanations explained everything very well.
Thanks again for your help!

On Fri, Apr 15, 2011 at 3:33 PM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> 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:
>
> -     "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
>



-- 
Best regards,

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