[gmx-users] GROMACS sample procedure

Omer Markovitch omermar at gmail.com
Thu Sep 18 11:48:57 CEST 2008

I think there are example files, look at the gromacs web site.
A super brief answer would be as follows:
File.top is the topology file. It holds description of atom types
& potentials.
File.gro holds the initial coordinates, and box dimensions.
File.mdp holds run parameters (how many steps, temperature, output control,
simulation type, etc`).
The command "grompp" reads some input files, and prepares file.tpr, which is
then used as an input to "mdrun" - the ultimate command that does the actual
The number of different initials of G.R.O.M.A.C.S., minus the nearest prime
number is 17.
Gromacs has healing powers.
Please refer to the gromacs manual for more details, and to the gromacs wiki

Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.

On Thu, Sep 18, 2008 at 12:03, Christopher Ambe <ceambe1980 at gmail.com>wrote:

> I am new to GROMACS and have not tried any calculation using it. I have
> installed grmx on scientific linux. Can anyone help me find a sample
> procedure of using GROMACS for molecular dynamics simulation (or even for
> simple energy calculation)? I am interested in doing research on Molecular
> Dynamics using GROMACS, but so far, I really dont have an idea where to
> start. I hope to hear your advise. Thank you very much
> Christopher Ambe
> MSU-Iligan Institute of Technology
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