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

From: Mark Williamson <>
Date: Wed, 01 Feb 2012 22:35:10 +0000

On 01/02/2012 21:13, Gustavo Seabra wrote:
> 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

Thank you. I do not envisage this replacing the normal mdout file; more
a machine readable augmentation to it, in the form of an extra,
independent, output file (with the possible option of automatically
zipping it at the end of the calculation..)

> future code-changes or additions? Would any newcomer have to learn CML
> and implement a CML output routine along with whatever work they are
> doing?

With reference to the source code, the FoX library takes care of most of
this difficulty; one generally just calls set subroutines from the FoX
module. There is a very good tutorial on how to implement FoX (using
WXML) in existing MD code, here:

Hence, anyone looking to add CML output for a new feature, should be
able to follow the example on that page.

I think the key thing at the moment is developing an AMBER dictionary ( ). This is an example one from SIESTA:

There are more examples of dictionaries in:

I'm currently working on getting a basic AMBER one, and someone adding
something new in future may need to add something to this dictionary.



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Received on Wed Feb 01 2012 - 15:00:02 PST
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