[gmx-users] Toy input system - MD simulation

Justin Lemkul jalemkul at vt.edu
Wed Jan 9 15:03:09 CET 2013

On 1/9/13 6:25 AM, 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?

You can find a large number of common molecules (both coordinates and 
topologies) on http://virtualchemistry.org/.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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