Executables (located in directory ../bin/):
| EXECUTABLE | PLATFORM and USAGE |
| sda | SGI IRIX executable of simulation program |
| sdaa | DEC ALPHA executable, uses ascii grids |
| sdabf | SGI IRIX executable of Boltzmann factor computing program |
Programs:
| PROGRAM | DESCRIPTION |
| sda.f | the simulation program. |
| sdabf.f | the sampling program |
Include files:
| INCLUDE | DESCRIPTION |
| maxdim.inc | defines array sizes |
Files, containing subroutines:
| MAIN SUBROUTINE | ACTION |
| bdmov.f | does basic Brownian dynamics move |
| bdrot.f | rotates the protein 2 |
| bdrotI.f | rotates the protein 1 |
| boost.f | handles boosts |
| cross.f | computes cross-product of 2 vectors |
| dsener.f | computes energy of desolvation grid - charge interactions |
| dsrpgrids.f | reads desolvation grids |
| dsrpgridsa.f | reads desolvation grids (ascii) |
| eener.f | computes energy of grid-charge interactions |
| eenerv.f | as above, handles variable grid spacing |
| eenerq.f | as eener.f, but for charge-charge treatment (iforce=2) |
| eforce.f | computes forces of grid-charge interactions |
| eforcev.f | as above, handles variable grid spacing |
| eforceq.f | as eforce.f, but for charge-charge treatment (iforce=2) |
| eschk.f | handles boundaries at c-surface (escapes) |
| exchkh.f | performs exclusion (overlap) check |
| incr.f | select the time step. |
| mkchpar.f | reads in charges |
| mkex1parh.f | constructs exclusion matrix of protein 1 |
| mkex2par.f | selects surface atoms to represent protein 2 |
| mkrxnpar.f | reads reaction atoms |
| mkrxnparC.f | the same for the case icomm=3 (independent pairs) |
| nacct.f | computer time account routine |
| rndmr.f | generates various random numbers |
| rpgrids.f | reads in 2 binary potential grids |
| rpgridsa.f | the same as above, reads ascii grids |
| rpgrids1.f | reads 1 binary potential grid |
| rpgrids1a.f | the same as above, reads ascii grid |
| rxncrt.f | checks reaction criteria when icomm=1 |
| rxncrtE.f | checks reaction criterion based on interaction energy (not used) |
| rxncrtP.f | checks reaction criteria when icomm=2 |
| rxncrtPC.f | checks reaction criteria when icomm=3 |
| uorient.f | generates random orientations |
| writg.f | writes grid to a file |