[gmx-developers] Testing an integrator in MD

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Tue Jun 26 21:04:27 CEST 2007

> Dear Gromacs Developers -
> Thanks for your responses regarding my question about implementing a
> new integrator in GROMACS and other MD codes.  My follow up question is
> this: If you were reading a paper that was introducing a new
> integrator, what kind of tests/data/analysis on what kind of systems
> would you need to see in order to decide about its validity and
> usefulness as a general purpose MD integrator?  As you can probably
> tell, I'm looking forward to designing and running these experiments,
> but I thought I had better ask the people who would potentially be
> using the results, which results in particular they would like to see,
> first, before I went off and did something that was
> irrelevant/unhelpful on accident.  I'd be open to biological, as well
> as materials, examples.  I've heard many people say energy conservation
> is important.  Is that always true?  What other parameters/phenomena
> should I be monitoring? Please try to be as specific as possible.

I would also suggest a reference (perhaps not so easy to find...):

Berendsen and van Gunsteren - Practical algorithms for dynamics  
simulations - p. 43-65
Proceedings of the International School of Physics "Enrico Fermi"
North Holland Physics Publishing


Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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