############################################################# ## Minimization and equilibration of CaliforniaSeaLionApoA1 ## bound to lipid ## ############################################################# # Reduces CaliforniaSeaLionApoA1 lipid complex to create rHDL-100 ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/CSApoA1100Ionized.psf coordinates C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/CSApoA1100Ionized.pdb set outputName CSApoA1100Final set temperature 310 firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_prot.prm C:/Users/tig_m/Documents/ThesisProjectMDSimulations/PyModModels/CaliforniaSeaLionApoA1/LipidBound/par_all36_lipid.prm 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 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Periodic Boundary conditions cellBasisVector1 129.0 0 0 cellBasisVector2 0 75.0 0 cellBasisVector3 0 0 39.0 cellOrigin 3.3 35.0 -52.0 wrapAll on #PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 130 #PMEGridSizeY 76 #PMEGridSizeZ 40 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for 2fs steps useFlexibleCell no ;# no for water box, yes for membrane useConstantArea no ;# no for water box, yes for membrane 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 2500000 ;# 5ns