[gmx-users] Parameter file

[Tsjerk Wassenaar]

Hi Fernando,

Have a look at the two parameter files and see in which regard they are
different, for indeed they are. Energy minimization is a distinct process,
for which you need specific settings in the .mdp file and also have other
control parameters. One of the most important settings concerns the
integrator, for which you can choose several integrators for energy
minimization (e.g. steep, l-bfgs), molecular dynamics (md) and others (check
the manual).

Cheers,

Tsjerk

On 10/4/05, MGiò <magiofer at gmail.com> wrote:
>
> HI!
>
> On 10/4/05, Fernando Mattio <mattiofer at gmail.com> wrote:
> >
> > Dear gromacs users,
> >
> > I have doubts about parameter file: Should I use the same parameter file
> > before and after the energy minimization or do I have to change it?
>
>
> do you mean the same parameters fo mechanics and dynamics? you have to
> change your .mdp, of course. you have to use md as the integrator and set
> temperature and temperature coupling method, at least, if you want to run
> NVT MD.
>
> And if I create a solvent box do I have to change anything in my parameter
> > file?
>
>
> usually I set different energy groups in presence of the solvent (Protein
> and SOL)
>
> I am following the Introduction to Molecular Dynamics course on
> > http://md.chem.rug.nl/education/mdcourse2004 and in this course they
> > used 2 different parameter files... That´s why I am asking these things.
>
>
> anyway the fullmd_sol.mdp that you find in the course you're following is
> clear and complete.
>
> Thank you very much in advance!
> > Fernando Mattio
> >
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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