[gmx-developers] Toy input System - MD simulation

Maria Astón Serrano m.aston.serrano at gmail.com
Wed Jan 9 11:43:03 CET 2013


I am new at this and I am working with the constraints algorithms used in a
MD simulation.
I would like to now how they work, what type of coordinates they use and
also to identify
some variables.

For that, I am trying to do a simulation with a toy input system, like
methane or ethane but I am
having some troubles: I started with a methane PDB file and *pdb2gmx* but I
got errors, I tried with
a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top
but I also got errors, ...

I know it is a very open-question but, could you help me? What would you
recommend me?
Do you have a toy input system?

Thank you very much,

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