[gmx-users] how to set the MD parameters?
mario_orsi at hotmail.com
Tue Feb 10 18:04:00 CET 2004
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
-mario orsi, student of "Politecnico di Milano", Italy.
"I'm very fond of music. Especially Beethoven." - a clockwork orange
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