[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 
>> tutorials).
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.
> Mark
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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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