Re: [AMBER-Developers] Possible CML support in PMEMD output

From: Gustavo Seabra <>
Date: Wed, 1 Feb 2012 16:13:07 -0500

Hi Mark,

That's some interesting work. My guess is, as long as we still have
the regular human-readable output file, that seems actually a pretty
nice addition. However, how is it going to work for any possible
future code-changes or additions? Would any newcomer have to learn CML
and implement a CML output routine along with whatever work they are

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417

On Wed, Feb 1, 2012 at 2:21 PM, Mark Williamson <> wrote:
> Dear all,
> I'm playing with adding CML output support into PMEMD on a local git
> branch. Here are more details on what I've been doing and why:
> The implementation is quite easy since all the work is done via the FoX
> library; I'm essentially piggy-backing any writes to the mdout file and
> outputting to an extra file called "cml", in XML. There is an example
> output from PMEMD on the site as well.
> One thing I can see instantly useful is that the output could be machine
> checked, and in the context of the AMBER tests, this could prevent many
> false positives with comparing small numerical differences. Other
> benefits include automated extraction of data from large numbers of
> simulations, automated visualisation of results (see some of the
> examples on the webpage) and it can facilitate comparison of a FF's
> implementation in different MD engines.
> Generally, what do people make of this? Would this be a useful addition?
> Any feedback or comments would be very useful.
> Regards,
> Mark
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Received on Wed Feb 01 2012 - 13:30:03 PST
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