#Simulation with 2 Indodi Molecule (Minimization) #------------------------------------------------------------ #Adjustable Parameters #------------------------------------------------------------ set temperature 0 set outputname Ind set inputname NID firsttimestep 0 numsteps 1000 #------------------------------------------------------------ #Specify a new job with AMBER force field #------------------------------------------------------------ amber on; parmfile NID.top; if {1} { ambercoor NID.crd; temperature $temperature cellbasisvector1 72. 0. 0. ; cellbasisvector2 0. 78. 0. ; cellbasisvector3 0. 0. 39. ; cellorigin 38. 41. 21. ; } #------------------------------------------------------------ #Continuing a job from the last simulation #------------------------------------------------------------ if {0} { coordinates $inputname.coor; velocities $inputname.vel ; extendedsystem $inputname.xsc ; #cell dimensions } #------------------------------------------------------------ #Continuing a job from the restart files #------------------------------------------------------------ if {0} { binCoordinates $inputname.restart.coor; binVelocities $inputname.restart.vel ; extendedsystem $inputname.restart.xsc ; # cell dimensions } #------------------------------------------------------------ #Simulation parameters #------------------------------------------------------------ wrapwater on; #wrap water to central cell wrapall on; #wrap other molecules too wrapnearest off; #use for non-rectangular cells #------------------------------------------------------------ #Force field parameters #------------------------------------------------------------ #1-2 1-3 pairs are excluded, 1-4 pair will be modified exclude scaled1-4 ;# for amber force field #modify electrostatic interaction between 1-4 pairs 1-4scaling 0.833333 ;# 1/scee scnb 2 ; #1-4 vdw interactions are divided by scnb cutoff 20.; #electrostatic and VDW interaction switching off; #Amber does not use switching functions #switchdist 10. pairlistdist 23. #------------------------------------------------------------ #Integrator Parameters #------------------------------------------------------------ timestep 0.5;# 1fs/step rigidBonds none; #Nonbonded interaction must be calculated at least every 2 fs nonbondedFreq 1 ; #nonbonded forces every step # the product of fullElectFrequency and timestep < 4.0 # if rigidBonds all or molly is not specified fullElectFrequency 2 ;#PME every other step stepspercycle 10 ;# redo pairlistdist every 10 steps #------------------------------------------------------------ #PME (for full-system periodic electrostatics) #------------------------------------------------------------ if {1} { PME yes PMEGridSizeX 72 PMEGridSizeY 80 PMEGridSizeZ 40 } #------------------------------------------------------------ #Constant Temperature Control #------------------------------------------------------------ if {1} { langevin on ;#langevin dynamics langevinDamping 1 ;#damping coefficient (gamma) of 5/ps langevinTemp $temperature;#random noise at this level langevinHydrogen off;#don't couple langevin bath to hydrogens } #------------------------------------------------------------ #Constant Pressure Control (variable volume) #------------------------------------------------------------ if {0} { useGroupPressure no ;#needed for rigidBonds # no---Pressure can be calculated using either the atomic virial and # kinetic energy or a hydrogen-group based pseudo-molecular # virial and kinetic energy # yes--required in conjunction with rigidBonds, needed for 2 fs steps # fluctuates less useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;#in bar -> 1 atm langevinPistonPeriod 100. ;#oscillation period around 100fs langevinPistonDecay 50. ;#oscillation decay time of 50fs langevinPistonTemp $temperature;#should be positive } #------------------------------------------------------------ #Output #------------------------------------------------------------ outputName $outputname binaryoutput no restartfreq 50 ;# 50steps = every 0.050ps dcdfreq 50 ; xstFreq 50 ; outputEnergies 50 ; outputPressure 50 ; outputtiming 50 ; #------------------------------------------------------------ #Execution script #------------------------------------------------------------ #Minimization minimize 100 reinitvels $temperature run 1000 ;# 1ps