[gmx-users] Energy minimisation

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 4 09:06:48 CET 2007

Hi Jestin,

As I said, the last line in the .gro file codes for the box. So, you have a
singular box! You probably did something wrong with editconf. Did you give
it box dimensions at all (-box/-d). Have a look at the help: editconf -h

Besides that, do have a look at the procedure you used to obtain the
topology and such. You shouldn't have a non-integer total charge, as Justin
pointed out.



On 4 Dec 2007 07:36:32 -0000, JMandumpal <jesbman at rediffmail.com> wrote:

> Dear users,
> What I see the difference between the .gro file given at the examples in
> the tutor directory and my own .gro file is that
> the last lines gives 0.000 0.000 0.0000 in my file and in the examples it
> is not.
> I assume it is the dimension of the box, isn' it?
> I built up the gro file using editconf -f *.pdb file.
> regards
> Jestin  Mandumpal
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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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