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
