[gmx-developers] Toy input System - MD simulation

Gerrit Groenhof ggroenh at gwdg.de
Wed Jan 9 11:51:50 CET 2013

This is more a question for the user list.
To learn about the algorithms, you can start reading the Shake and Lincs papers.


On Jan 9, 2013, at 12:43 PM, 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
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