Re: Changing functions without recompiling

From: Cole Gleason (
Date: Mon Oct 18 2010 - 21:27:27 CDT

On Mon, Oct 18, 2010 at 8:42 PM, Joshua Adelman <> wrote:
> Hi Cole,
> As Axel suggested, there are other MD packages that handle this type of
> functionally without modification. An alternative to tabulating the
> functions is a direct mathematical expression parser like the one that is
> found in OpenMM (, which is called Lepton
> (
> Depending on what types of simulations you are planning on running, you
> might want to give OpenMM a try (or at least a look) since it allows you to
> write custom force-field terms and has a nice python wrapper. It's not a
> full-fledged MD code, in that you basically have to assemble the parts from
> scratch, and the CPU mode is largely unoptimized, but if you have access to
> any decent GPUs, it can be quite fast even with the custom force calls. I've
> been using it mostly to run some coarse-grained simulations, but you can run
> fully atomistic biological systems as well. It may not be the right tool for
> this job for any number of reasons, but I just wanted to throw out another
> option.

I've tried at OpenMM, but they seem to be mostly GPU based like you
said. We don't really have any decent GPUs, which is why I went the
CPU MPI route.

> Back in NAMD 2.6, I hacked in some custom force calls, based on the
> GlobalMaster routines, but that only ran on the head process and you had to
> recompile each time you made changes to the underlying functional form.
> Best of luck,
> Josh

Cole Gleason
Student, Marmion Academy

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