01mi.in

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 #input files (section 3.2.1)
 coordinates GP41.WILD_t20.new.solvated.pdb     #name of coordinate (pdb) file
 structure GP41.WILD_t20.new.solvated.psf      #psf file
 parameters  par_all27_prot_lipid.prm #parameter file
 paratypecharmm  on    #specifies if this is a charmm force field (on or off)
 #velocities Z-VELOCITIES    #velocity file for a restart note that in a restart delete the temp
 #
 #output file (section 3.2.2)
 outputname 01mi    #specifies the prefix for the output files
 binaryoutput  no    #activates binary output (yes=binary)
 DCDfreq   1000     #number of timesteps between the writing coordinates
 #
 #standard output (section 3.2.3)
 outputenergies  1000    #number of timesteps between energy output
 outputTiming  1000    #number of timesteps between timing output
 #
 #timestep parameters (section 5.3.1)
 firsttimestep  0    #frame number where the simulation starts
 timestep  1    #length of each step in fs
 stepspercycle  20    #how often the interacting particle lists are updated
 #
 #space partitionin (section 5.3.2)
 cutoff   12    #non-bonded cutoff
 switching  on    #smoothing function for ES and VDW
 switchdist  10    #distance at which the smoothing function is applied
 pairlistdist  16    #distance >= switchdist for atom pairs to be included in the pairlist
 margin   8    #see section 5.3.2
 #
 #basic dynamics (section 5.3.3)
 exclude   scaled1-4   #which bonded atom pairs are excluded from non-bonded calculations
 temperature 310    #INITIAL temperature of the simulation note delete on restart
 1-4scaling  1.0     #1.0 for Charmm, 0.833333 for Amber
 rigidbonds  water    #controls how shake is used
 rigidTolerance  0.00001    #allowable bond length error for shake
 #
 #PME parameters (section 5.3.5)
 PME   yes    #turns PME on or off (yes=on no=off)
 PMEGridSizeX  72    #number of grid points in X dimension
 PMEGridSizeY  72    #number of grid points in Y dimension
 PMEGridSizeZ  216    #number of grid points in Z dimension
 #
 #constraints (section 6.1)
 constraints  on    #on or off
 consref GP41.WILD_t20.new.solvated.pdb     #pdb file with restraint reference positions
 conskfile GP41.WILD_t20.restraint01.pdb     #pdb file with force constant values
 conskcol  B
 #
 #temperature control and equilibration (section 6.3)
 langevin      on  #turns langevin dynamics on or off
 langevinTemp  310 #temp to which langevin dynamics will be adjusted
 langevinDamping  1    #damping coefficient for langevin dynamics
 #
 #periodic boundry conditions (section 6.4.3)
 cellbasisvector1 67.2 0 0  #defines the first periodic boundary
 cellbasisvector2 0 65.1 0  #defines the second periodic boundary
 cellbasisvector3 0 0 201.1 #defines the third periodic boundary
 cellorigin -17.058 -16.730 -59.465 #defines the xyz location of the center of the box
 #extendedSystem Z-EXTENDEDSYSTEM  #defines file which contains the PBC info from previous runs
 wrapwater on    #wraps the waters to one box.
 wrapall   on    #wraps every contiguous cluster of bonded atoms
 wrapNearest  off    #wraps coordinates to the nearest image to the origin
 #
 #pressure control (section 6.5)
 langevinPiston  on    #turns on constant pressure
 langevinPistonTarget 1.01325    #target pressure
 langevinPistonPeriod  200    #period over which the pressure is averaged in fs
 langevinPistonDecay   100    #damping time scale in fs
 langevinPistonTemp    310    #should be equal to langevin temp
 #
 #equilibration
 #run Z-NSTEPS
 minimize 1000