04md.in

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#input files (section 3.2.1)
coordinates 03mi.coor     #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 04md    #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.restraint04.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 03mi.xsc       #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 500000
#minimize Z-NSTEPS