Re: Debugging and Force Checking?

From: Jérôme Hénin (
Date: Mon Jul 20 2015 - 12:42:20 CDT

Hi Brian,

We have such a script to test analytical gradients of scripted collective
variables in the colvars module. See the code there:

Note that this is handling vectors of vectors, so there is a little legwork
to get everything transposed according to the convention used by the
colvars module.


On 20 July 2015 at 16:32, Brian Radak <> wrote:

> I can't seem to find this in the manual; how does one turn on debug output
> in NAMD? Is it via a compile flag or is there an input option?
> I am also wondering if anyone has a routine to test analytical versus
> numerical derivatives. Presumably this could be somewhat simply implemented
> in a tcl script. If there is no such resource, would there be interest in
> producing one?
> Regards,
> Brian
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail:

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