[gmx-users] Energy minimisation

[Tsjerk Wassenaar]

Jestin,

Please don't use all capitals. As Mark has pointed out several times, that's
considered shouting. You're probably frustrated that things don't work
according to your expectations, but the frustration comes from you not
knowing what your doing. Don't blame us for that, go read a manual.

If something is not specified in the .mdp file, the default is used. One
thing not specified in your .mdp file is the way to treat PBC, so grompp
will want to use xyz. When using (standard) PBC, the cut-off should not be
longer than half the box length, as you should be aware if you have read MD
basics. Apparently, you're using a cut-off length longer than allowed for
your box (says grompp). You say it's 20.1 A to all sides, which should be
okay when using a 1.0 nm cut-off. I suspect the last line of your .gro file,
which describes the box dimensions, says something else. You should verify
that and paste us the last line of the .gro file if you can't see anything
wrong with it.

Cheers,

Tsjerk

On 3 Dec 2007 00:19:25 -0000, JMandumpal <jesbman at rediffmail.com> wrote:

> Dear Justin,
>
> Thanks for the response.
>
>
> This is my input file (em.mdp) which contains parameters for doing energy
> minimisation.
>
> cpp            = /lib/cpp
> define        = -DPOSRES -DFLEX_
> constraints    =  none
> morse          =  no
> integrator    = steep
> nsteps        = 2000
> ; Energy minimizing
> emtol          = 100
> emstep        = 0.00001
> nstcomm        = 1
> ns_type        = grid
> rlist          = 1.0
> rcoulomb      = 1.0
> rvdw          = 1.0
> Tcoupl        = no
> Pcoupl        = no
>
>
>
> MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM.
>
>
> THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY
> MINIMISATION.
>
> http://www.gromacs.org/component/option,com_wrapper/Itemid,84/
>
>
>
>
>
> regards
> Jestin
>
>
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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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