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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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