#forcefield paratypecharmm on parameters ../../TOOLS/par_all27_prot_lipid-a.prm #molecules structure all1.psf coordinates all1.pdb bincoordinates equ3.restart.coor #binvelocities equ2.restart.vel extendedSystem equ3.xsc temperature 310 reassignFreq 100 reassignTemp 25 reassignIncr 25 reassignHold 310 #constraints constraints on consref equ1-c3n.pdb # protein_only.coor conskfile equ1-c3n.pdb # protein_cons.pdb conskcol B #temp & pressure coupling langevin on langevinTemp 10 langevinDamping 1 #useGroupPressure yes #useFlexibleCell no #LangevinPiston on #LangevinPistonTarget 1 #LangevinPistonPeriod 200 #LangevinPistonDecay 500 #LangevinPistonTemp 10 #output outputname equ3n outputEnergies 10 restartfreq 500 DCDfreq 500 binaryoutput no binaryrestart yes outputTiming 100 wrapAll on wrapNearest on #integrator timestep 1 nonbondedFreq 1 fullElectFrequency 4 stepspercycle 20 #approximations rigidBonds all rigidTolerance 0.00000001 cutoff 12 switching on switchdist 10 pairlistdist 14 margin 3 exclude scaled1-4 1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber PME on #cellBasisVector1 76. 0 0 #cellBasisVector2 0 76.5 0 #cellBasisVector3 0 0 76 PMEGridSizeX 80 PMEGridSizeY 80 PMEGridSizeZ 100 #minimize 1000 run 25000