[gmx-developers] Toy input System - MD simulation

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 9 19:29:11 CET 2013

On 2013-01-09 11:43, 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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