[AMBER-Developers] Possible CML support in PMEMD output

From: Mark Williamson <mjw.mjw.name>
Date: Wed, 01 Feb 2012 19:21:02 +0000

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.



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Received on Wed Feb 01 2012 - 11:30:04 PST
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