Re: editing the code of the non bonded pair potentials

From: Axel Kohlmeyer (
Date: Fri Aug 30 2013 - 13:59:26 CDT

On Fri, Aug 30, 2013 at 8:47 PM, Kenno Vanommeslaeghe
<> wrote:
> On 08/30/2013 10:10 AM, Axel Kohlmeyer wrote:

> Axel, sorry for going a bit on a tangent here, but purely out of educational
> interest, can you give a pointer to one (or more) from the top of your head?

depends on what kind of system you want to simulate.

if you just want a toy MD code for simple single type lennard-jones
system with nve verlet integrator, you can easily write one yourself
based on what several books on MD suggest. i wrote one myself for
teaching optimizing and parallelizing a scientific code (and an LJ MD
has about the smallest and simplest compute kernel around that you can
compare to a real life application).

> A quick Google search turned up toyMD, but since you appear to be more
> knowledgeable in these things than I am, I'd like to know your opinion.

if you are looking for something more serious and applicable for read
world simulations, i would suggest something like Tinker or LAMMPS or
a toolkit like ASE or OpenMM.


> Cheers,
> Kenno.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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