# molecular system paraTypeCharmm on parameters par_all32_lipid.prm coordinates eq1.out.coor structure top.psf set runn full_abf firsttimestep 75000 temperature 303 set temperature 303 # force field exclude scaled1-4 1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber # nonbond interactions switching on switchdist 8.5 cutoff 10 pairlistdist 12 # integrator timestep 1 nonbondedFreq 1 FullElectFrequency 4 stepspercycle 20 #For Cubic Box Simulation cellOrigin 6.969 -12.609 -4.868 cellBasisVector1 55.4175 0.000 0.000 cellBasisVector2 0.000 67.5078 0.000 cellBasisVector3 0.000 0.000 70.9368 PME on PmeGridsizeX 58 PmeGridsizeY 70 PmeGridsizeZ 74 margin 5 #---------------------------------------------------- # output outputname ${runn}.out outputenergies 1000 outputtiming 1000 binaryoutput no dcdfreq 1000 # how often we output trajectories. wrapall on wrapNearest on # for restarting: restartname ${runn}_restart restartfreq 1000 restartsave no rigidBonds all rigidTolerance 1.0e-6 constraints on consRef fix_atoms.pdb consKFile fix_atoms.pdb consKCol B langevin on langevinDamping 10 langevinTemp 303 langevinHydrogen on langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 303 useGroupPressure yes # smaller fluctuations useConstantRatio no # fix shape in x-y plane output ${runn} # ABF SECTION set ABFdir ./abf-1.8 source ./abf-1.8/abf.tcl # ORDER PARAMETER abf coordinate distance abf abf1 8846 abf abf2 9876 abf xiMin 5.0 abf xiMax 34.0 abf dxi 0.1 # SAMPLING abf fullSamples 500 abf dSmooth 0.1 abf forceConst 10.0 abf writeXiFreq 100 # OUTPUT abf outFile full_run.abf run 250000