Trajectory file format with box information. #1
Description
Hi there,
It would be nice to start using this shiny interface for talking about code. :)
One of our current goals is to carry out the mutual AMOEBA parameterization with condensed phase properties using TINKER as the MD engine. In order to do this, TINKER’s “analyze” program needs to rapidly loop over the MD trajectory and recompute the energies, but the .arc file contains no box information. The current solution (using unmodified TINKER) would involve writing a new .key file and calling “analyze” for each frame, which would be too time-consuming because "analyze" needs to be loaded into memory for each frame. It would be nice if the box information could be loaded as the program iterates over the trajectory.
My current solution involves modifying TINKER to write a separate “.box” file during the molecular dynamics, and when TINKER loops over the trajectory using “analyze”, it reads the .arc and .box files at the same time. This is sort of a clunky solution, and I can’t always keep my version up-to-date with the official code. Furthermore, I’m not sure if you think it’s a good idea to bundle the modified TINKER with ForceBalance, since the licenses are different.
Because of this, I’m hoping that we could revisit the topic of writing boxes to the .arc file. My idea would be adding an option to the key file, perhaps “new-archive” – it would then write a new .arc format with box information (just one extra line) which TINKER would still understand, but external codes such as VMD will no longer understand it. We can use a new file extension, perhaps “arx” or something similar. If both “archive” and “new-archive” are specified, then it will write both formats, though the storage will be doubled.
This way we could introduce the new archive format without breaking anything. Let me know what you think.