[gmx-users] how to set the MD parameters?

[mario orsi]

Hi everybody,
I've just started using Gromacs (so far I did the tutorial and been playing 
around a little); the purpose of my project is to study a protein from a 
mechanical point of view. So I guess I'll have to perform elongations 
(constraining distances) and take care of the energy variations. However, 
firstly an optimization of the molecule is needed (by the way, I'm working 
with the PDB 1QUU). Got a (likely silly) question about MD parameters. The 
gmx manual says:

"A sample .mdp file is available. This should be appropriate to start a 
normal simulation. Edit it to suit your specific needs and desires."

How can you do that? I mean, practically, how to create or modify a .mdp 
file?

Thanks, ciao
-mario orsi, student of "Politecnico di Milano", Italy.

"I'm very fond of music. Especially Beethoven." - a clockwork orange

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