[gmx-users] Parameter file

MGiò magiofer at gmail.com
Tue Oct 4 10:30:50 CEST 2005


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

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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