[gmx-users] Toy input system - MD simulation

Maria Astón Serrano m.aston.serrano at gmail.com
Wed Jan 9 12:25:08 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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