Release of beta version of 0.3 series

[Shun Sakuraba]

Dear list,

New version of ERmod software package, 0.3-beta1, is released.
https://sourceforge.net/projects/ermod/files/ermod-0.3%20(experimental)/

This is a "beta" version of 0.3 series. All planned major updates are now implemented in the program.
After implementing minor updates we will soon release version 0.3 as stable series.

List of major features implemented in 0.3 (from 0.2):

* Supported AMBER input (very experimental). New tools are stored under tools/AMBER.
Users must provide NetCDF trajectory - see AMBER manual for how to generate binary trajectory file.
Also, users must change file extension to ".nc", and make (or copy) netcdfplugin.so manually.
* Reordering atoms in trajectory is much easier in 0.3.
* A script to separate residues in protein as "solvents" is added (under tools/mol_dissect).
* Non-orthogonal periodic box is now correctly handled.
* Insertion scheme is now much more flexible - weighted insertion around best-fit structure and overall system are now possible.

Thank you!
--
Shun SAKURABA, Ph.D.
Postdoc @ Molecular Modeling & Simulation Group, Japan Atomic Energy Agency