2017-04-13 14:34 GMT-06:00 Alireza Moradzadeh <a.mr...@gmail.com>:
> Let me be more specific, for example in relative entropy we can calculate
> average of AA esemble using rdf the second method is to use mapped AA
> trajectory and calculate energy based on trajectory! however, this method is
> not efficient so current implementation uses RDF. however, for parameters in
> my mind I need to have access to energy of each frame of AA trajectory but
> in csg_application we have:
>
>
> _traj_reader =
> TrjReaderFactory().Create(_op_vm["trj"].as<string > ());
> if (_traj_reader == NULL)
> throw runtime_error(string("input format not supported:
> ") + _op_vm["trj"].as<string > ());
> // open the trajectory
> _traj_reader->Open(_op_vm["trj"].as<string > ());
>
>
> and then we use worker and evalconfiguration to calculate different
> properties. Now I want to do similar thing for mapped AA trajectory. I am
> looking for a way to evaluate mapped AA (MAA) and CG in series.
>
> The way that I am seeking which is not efficient is to run csg_xxx.cc once
> for CG save dlamda and d2lamda and then run it again and use saved
> information to evaluate the other trajectory! But it is not efficient and
> systematic. For sure, there is a way to do all these stuff with one run in
> series!
Like I said csg_map does a hybrid topology, which you could use for
analysis in your case:
<https://github.com/votca/csg/blob/master/src/tools/csg_map.cc#L84>
You could even put most of the stuff in the BeginEvaluate() for better
performance.
But by the end of the day, you will have to play a bit around with
code yourself as nobody has done something similar, yet.
Plus, the work might not worth it due to the fact that at most you can
save a factor 2 (in comparison to running your analysis tool twice).
Christoph
>
> Thanks,
> Alireza
>
> On Thursday, April 13, 2017 at 8:43:01 AM UTC-5, Christoph Junghans wrote:
>>
>> 2017-04-12 21:51 GMT-06:00 Alireza Moradzadeh <a.m...@gmail.com>:
>> > Dear All,
>> >
>> > I need to have access to All-Atom MD and Coarse-Grained MD simulations
>> > and
>> > do some calculation based on frames trajectories. Current version of
>> > votca
>> > using csgapplication only loads one trajectory file using
>> > TrajectoryReader *
>> > _traj_reader, However, I need to define another worker and trajectory
>> > reader. I am not sure if I have to change csgapplication or try to
>> > implement
>> > a new thread, worker and evalconfiguration just for my own function
>> > (lets
>> > say csg_xxx.cc) .
>> > In other words, I need to do some calculation on CGMD and AAMD to
>> > calculate
>> > some properties, so I want to have access to both of them in the same
>> > program csg_xxx.cc and I want it to be parallel.
>> >
>> > Any recommendation is highly appreciated!
>> Have a look at the code of csg_map:
>> <https://github.com/votca/csg/blob/master/src/tools/csg_map.cc>
>> and especially on how the "hybrid" option is implemented.
>> This option is using the coarse-grained and atomistic trajectory at
>> the same time.
>>
>> Christoph
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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