[gmx-users] infinitive force acting on atom during

Sivashangari Gnanasambandam g0501135 at nus.edu.sg
Tue Jan 16 06:28:07 CET 2007

Dear all,

I run the NPT (anisotropic) for the urea-water system. After the md run
the pressure is not closer to 1 bar but in terms of 100. Suggest me the
corrections in my parameter file. 

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Monday, January 15, 2007 7:54 PM
To: Discussion list for GROMACS users
Subject: Re: Re: [gmx-users] infinitive force acting on atom during

Hi Joern,

In any case, you want to first perform an energy minimization in vacuum
to release the strain present in your starting structure. Only then can
you be sure that if you run into trouble after solvating your system, it
is caused by that. It may be that during solvation a solvent molecule is
misplaced, but that would more likely cause a "water molecule ... cannot
be settled" error. At this point, I would suggest to introduce an
additional step of energy minimization prior to solvation. If you still
run into trouble then, post again with new details and we can have a
more thorough look.

> Have you or anyone else got an idea of what goes wrong in my
> And another thing is (perhaps a stupid question ?!?): why is it better

> not to use a cubic box for the simulation ?

Not a stupid question. For one thing, the cubic box is a waste of
resources. The rhombic dodecahedron will give you the same minimum
distance between periodic images for 71% of the volume. There's an
additional advantage when using a rhombic dodecahedron. Because it
corresponds to the densest packing of a sphere, it ensures that you have
the same distribution of solvent all around your solute. With a cubic
box (or a rectangular box, or a truncated octahedron), you have an
uneven distribution and this can potentially affect the results obtained
from your simulation.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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