A new Q: major enhancements in version 4

After three years of stable operation and gradual improvement of Q version 3, we now take a leap to a new program.

New features include

A trajectory analysis program for measuring geometrical properties on all recorded co-ordinate sets in trajectory (and restart) files. You can calculate RMS coordinate deviation for any set of atoms, superimpose a set of atoms onto a reference structure and mesure any distances, angles and all bonded force field terms.
The trajectory files are written in DCD format (CHARMM trajectory format) which can be read directly by molecular visualisation programs, e.g. VMD, for trajectory animation and further analysis.
Huge savings of disk space are made possible by recording the trajectory of only a subset of the atoms of the simulated system.
Solvent and simulation sphere is now set up in topology preparation program and stored in the topology file, making Qdyn input simpler.
Any tri-atomic molecule may be used as solvent.
More flexible generation of PDB files by easily selecting any set of atoms.
Less editing of input structure PDB files is required by smarter recognition of separate molecules.
Improved generation of hydrogen atom co-ordinates: torsion angles to hydrogen atoms may be specified in the fragment library.
SHAKE can be applied to bonds to hydrogen atoms only.

Migrating to the new version

We did our best to keep the new version compatible with the old one. You need, however, to re-make your topology. This is easy since Qprep will still read the old topology. A couple of additions to the fragment library and force field parameters files are necessary for the new and more flexible SHAKE constraints.

How to get it

What's also new is that we are now licensing the program in a more formal way. You need to sign a license agreement to get the login information which will allow you to download the software. We will still distribute the software, complete with source code, free of charge to academic and other non-commercial users.