Brownian Dynamics Simualtion

We now have all the components in place to start our BD simulation. We do need the translational and rotational diffusion constants for barnase and barstar. I have calculated reasonable values which you should use (I want you to all have the same values), and they are in the input file below.

- use binary grid here     -------dseed
694.d0                                  <----- random seed
-----------------------------nrun,nprint
1000000,10000,0,4,4.0,0          <----- number of runs, log frequency
-----------------------------probes, thres     
2.0, 1.  1.10, 8.0
-----------------------------pdb1f,pdb2f
barnase.pdb                      <----- structure 1
barstar.pdb                      <----- structure 2
-----------------------------po1f,po2f
barnase.50mM.grd                 <----- potential grid 1
barstar.50mM.grd                 <----- potential grid 2
-----------------------------qef1f,qef2f
barnase.echa_R                   <----- effective charge set 1
barstar.echa_R                   <----- effective charge set 2
-----------------------------rxna1f,rxna2f
barnase.rxn                      <----- reaction site 1
barstar.rxn                      <----- reaction site 2
-----------------------------ic1fix,xc1, ic2fix,xc2
0,   0.000 0.000 0.000           <----- center of protein 1
0,   0.000 0.000 0.000           <----- center of protein 2
-----------------------------icomm, iforce, dind, aiostr
 3   1, 5.0,  0.
-------------------------------dm,dr,drI,irot2f
0.028  ,   4.018e-5,   4.018e-5,1       <----- diffusion constants
-------------------------------b,c
75., 200.                               <----- b and c surfaces 
-------------------------------rboost,novers
1.0,  150, 5.
-------------------------------dt1,swd1,dt2,swd2,rswd
8.0,   20.,    50.,   120.,   120.      <----- time steps 
-------------------------------win0,dwin,nwin: 
3.00,  0.25, 45, 0, 2                   <----- reaction windows

I've labeled the items in the input file that you should understand. Take this file and make sure of the following:

• Change the random seed to something of your own choosing, otherwise you will all run the exact same simulation
• You will perform 1,000,000 trajectories. Writing out results every 10,000 trajcetories is reasonable
• Make sure that the structures, grids, charges and reaction sites are correct and in the same order (protein 1 then protein 2, etc.).
• Change the centers to match the center of the potential grid. This information is in the APBS log file or can be found using psize.
• The diffusion constants should be fine.
• Keep these values for the b and c surfaces. These are outside the range of the electrostatic potential, so we can use the Smoluchowski result.
• We will take 8 ps time step when the proteins are close, and this will scale up to 50 ps time steps when the proteins are separated by 120 A or more. Don't change these values.
• The reaction site files specify atom pairs that form contacts on the two proteins. The reaction windows monitor these atom pairs and keep statistics for all distances between 3 A to 14 A (3 + 44*0.25).

Once you have edited the input file, you can start the simulation

sdap < barnase-barstar.inp > barnase-barstar.log &

A file runs.done will be updated every 50 trajectories so you can monitor the progress of the simulation. Once the run finishes, you need to analyze the log files.