[gmx-developers] grompp .mdp processing
David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 23 00:08:22 CET 2009
Mark Abraham wrote:
> Sander Pronk wrote:
>> Hi everybody,
>> I've made some changes to grompp (not committed yet) that:
>> - will allow the use of cpp-style #include and #define in .mdp files
>> (useful for setting up multiple similar simulations, but also for
I assume you have used the existing cpp library?
> That looks good to me. I also generate my .mdp files with scripts, but
> this feature would enable me to avoid that.
I'm not sure, nowadays one needs to do series of simulations anyway, so
scripting is a necessary evil.
>> - allows multiple assignments of .mdp parameters, through overrides so
>> that the last assignment is the one that counts.
> Doing so always and silently would be asking for trouble, however if
> they're only enabled with -m, and come with a note to the user when
> they've occurred, that should be useful in a few corner cases.
And it would reverse the current policy, that is first option goes,
implying that one may get different results with the same input.
Further, I feel a bit uncomfortable with extending the mdp files
further, because we should rather move away from the endless list of
options. I haven't thought this trough, but I would prefer to move to a
slightly more complex format that, however, is more user friendly.
Thinking of a folding editor file (xml springs to mind). It should still
be possible to generate using a script, but there are xml bindings for
Perl and Python as well.
>> Together, I feel this makes .mdp files a bit more useful in production
>> work and for tutorials/teaching (by using .mdp files with sane
>> defaults that can be included in very short .mdp files that contain
>> the settings for the topic at hand) and make scripting easier.
>> It should not break anybody's existing parameter files, but I think I
>> should give a heads up before I commit to cvs.
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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