new release for Browndye

[Gary Huber]

Dear Browndye users,

We have released a new version, the first since this summer.  Here's a partial list, as

seen in Fixes and Updates on the website.

 Added hydrophobic interactions
 Improved constraint algorithm
 Bug fix in pathway code
 Bug fix for case of flexible chain attached to core
 Changed polar desolvation force to match expression in SDA software
 Desolvation grids now exactly mirror electrostatic grids; used to be just inner grid
 Added polar desolvation force for chains
 Possible to specify Lennard-Jones parameters using epsilon and sigma
 Added some defaults to process_trajectory 

The two bugs mentioned were the most serious ones.  The pathway one was making multiple-thread simulations seg-fault, and the other bug was giving unbalanced position updates for chains attached to cores with rigid constraints.  Another bug was causing the rigid constraint algorithm to converge very slowly, but that has been fixed and the algorithm itself improved.

The hydrophobic interactions are based on those in SDA. Each atom now carries an approximate surface area, which is used in a pairwise model. (Mereghetti P, Gabdoulline R, and Wade RC.  Brownian dynamics simulation of protein solutions: Structural and dynamical properties.   Biophys. J. (2010) 99, 3782-3791). I still need to add those to bd_top, so it will set up those forces automatically. But you can use the program "get_areas" to add the atomic areas to the XML PQR file.

I decided to change the numerical factor for the polar desolvation force to match what is used in SDA; it has the same form but is weaker for most cases. (Gabdoulline RR and Wade RC .  On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f : Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.   J. Am. Chem. Soc. (2009) 131, 9320-9238). Also, the desolvation grids generated by bd_top now mirror the electrostatic grids.

The next large items on the future list are the addition of the ABSINTH force field, a very promising implicit solvent force field from the Rohit Pappu group, and the addition of a GB/SA force field, such as the one implemented in NAMD and other molecular mechanics packages.  Also coming soon, I hope, will be a method to compute equilibrium binding constants, without the use of an arbitrary reaction distance.     

Thanks,

Gary