To do on Monday (again)

1) Complete Trajectory::WriteInfo() routine with config information.
2) Complete Trajectory::Read() member for reading traj dirs.
3) Modify biosimzstats, biosimzapp and biosimzlab to adapt changes.
4) Test FileAttached class for path manipulations in BioSimzTest.
5) Test Trajectory in BioSimzTest.
6) Test all file-related functions are working normally.
7) Test CollisionSheet in simulations.

To do (Tuesday on):

8) Modify submission scripts adapting the changes made to trajectory management.
9) Set up simulations for barnase/barstar and ras/effectors.
10) Write code for parsing CollisionSheet into tables/svg graphs.
11) GUI improvement and manuscript preparation.

Also pending:

12) Prepare a figure for Paul's annual report on BioSimz.

!!!!!!!!!!!!!!

To do on Monday

Add event counter system to the collision solver to be able to serialise the binding event history of a trajectory. This is for future expansion on biosimzstats regarding reaction rate calculation.

Further investigation on how to calculate the rate constants (wrt BioSimz) needs to be carried out.

It has been suggested that for known interactions in MolView data plots, the centre-of-mass of the interface residues should be plotted instead of that of the whole protein.

Literature search for the "sticky" nature of protein-protein interactions should be performed.

To do in the evening

To do:

a) modify the variable name m_effDist to m_maxPtl in vdw and hbond forcefields
b) increase the vdw attraction to stabilise dynamic interactions.

Parameters for the OLD vdw settings

min distance: 2.99
attractive scale: 2.3