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

[Nguyen Hoang Phuong]

> 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?

practically, you go to :

http://www.gromacs.org/documentation/reference_3.2/online/mdp_opt.html

then you will see  "sample .mdp file is available", click at that
sentence, you will see how the sample.mdp file look like.

If you want to modify it, you should look at the "mdp opion-table of
contents" (same page) to see the meaning of parameters.

Phuong

>
> 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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