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- #############################################################
- ## JOB DESCRIPTION ##
- #############################################################
- # Minimization and Equilibration of
- # Aldosterone procesada
- #############################################################
- ## ADJUSTABLE PARAMETERS ##
- #############################################################
- structure ald.psf
- coordinates ald.pdb
- set temperature 310
- set outputname ald_wbi
- firsttimestep 0
- #############################################################
- ## SIMULATION PARAMETERS ##
- #############################################################
- # Input
- paraTypeCharmm on
- parameters ald.par
- temperature $temperature
- # Force-Field Parameters
- exclude scaled1-4
- 1-4scaling 1.0
- cutoff 12.0
- switching on
- switchdist 10.0
- pairlistdist 14.0
- # Integrator Parameters
- timestep 2.0 ;# 2fs/step
- rigidBonds all ;# needed for 2fs steps
- nonbondedFreq 1
- fullElectFrequency 2
- stepspercycle 10
- # Constant Temperature Control
- langevin on ;# do langevin dynamics
- langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
- langevinTemp $temperature
- langevinHydrogen off ;# don't couple langevin bath to hydrogens
- # Periodic Boundary Conditions
- cellBasisVector1 42.0 0. 0.0
- cellBasisVector2 0.0 44.0 0.0
- cellBasisVector3 0.0 0 47.0
- cellOrigin 31.0 29.0 17.5
- wrapAll on
- # PME (for full-system periodic electrostatics)
- PME no
- PMEGridSpacing 5.0
- #manual grid definition
- #PMEGridSizeX 45
- #PMEGridSizeY 45
- #PMEGridSizeZ 48
- # Constant Pressure Control (variable volume)
- useGroupPressure yes ;# needed for rigidBonds
- useFlexibleCell no
- useConstantArea no
- langevinPiston on
- langevinPistonTarget 1.01325 ;# in bar -> 1 atm
- langevinPistonPeriod 100.0
- langevinPistonDecay 50.0
- langevinPistonTemp $temperature
- # Output
- outputName $outputname
- restartfreq 500 ;# 500steps = every 1ps
- dcdfreq 250
- xstFreq 250
- outputEnergies 100
- outputPressure 100
- #############################################################
- ## EXTRA PARAMETERS ##
- #############################################################
- #############################################################
- ## EXECUTION SCRIPT ##
- #############################################################
- # Minimization
- minimize 100
- reinitvels $temperature
- run 500 ;# 1ps
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