Amber-MD
A new feature of CPPTRAJ, which might hopefully be interesting and useful...
Dear Thom; Dear Dan,
many sincere thanks for your prompt and truly helpful response!
In fact, I wouldn't like to add solely 'dumping' functionality to CPPTRAJ, just to produce further output files.
My actual idea would be as follows:
I would greatly appreciate EXTRACTING the already generated coordinate/velocity/force data from the NetCDF trajectory file to place them into some allocated memory areas, and work with them on the fly, so to speak.
In particular, I would like to look for the generic regression (e.g., some kernel regression) of the Forces and Velocities onto the Coordinates. This way, I expect getting the direct information as for the kinetic and potential energies of the system under study in 'their temporal development', so to speak.
Obtaining such an information ought to allow me learning about the generic capabilities of the polymeric system under study, when it is placed on the surface, into the nanoscopic 'cups' etc.
Getting the infos concerning the systems 'energetics', so to speak, is the first step, whereas the second important step ought to be the so-called factor analysis of the correlations among the atoms of the system and its couterion-water sheath. With this information at hand you might decide about the roles of the protein/DNA/sugar domains, the couterion-water sheath in the processes you are studying.
We have already applied such an approach (though, without the above-mentioned energetics!) to study the modalities of cyclodextrins' solubility in water:
http://www.sciencedirect.com/science/article/pii/S0009261401001609/pdfft?md5=25bd30a0b674235882cfc3e452d68654&pid=1-s2.0-S0009261401001609-main.pdf
With all this in mind I shall definitely add such a feature request to the cpptraj GitHub page... Moreover, I am presently thinking about the actual regression routines. The factor analysis of large & sparse correlation matrices might be accomplished with the routines from the ARPACK library, for example... Howbeit, I would anyway be ready for active collaborations with the CPPTRAJ authors...
Respectfully yours,
Evgeni
