[gmx-users] Toy input system - MD simulation

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 9 19:29:29 CET 2013

On 2013-01-09 12:25, Maria Astón Serrano wrote:
> Hello,
> 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,
> Maria

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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