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!
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 <[email protected]
> <javascript:>>:
> > 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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