################################################### # equilibration in water ################################################### # MD SETUP timestep 2.0 ##numsteps 1 # FLEXIBLE CELL useflexiblecell no # INPUT structure solvate.psf parameters /home/bits/Documents/FEP-tutorial-files/04.Binding-of-a-potassium-ion-to-18-crown-6/Test/par_all35_ethers.prm paraTypeCharmm on coordinates solvate.pdb bincoordinates equilibration.coor binvelocities equilibration.vel extendedsystem equilibration.xsc # OUTPUT outputenergies 100 outputtiming 100 outputpressure 100 binaryoutput yes outputname forward restartname forward restartfreq 100 binaryrestart yes XSTFreq 100 # DCD DCDfreq 500 DCDfile forward.dcd # PME PME yes PMETolerance 10e-6 PMEInterpOrder 4 PMEGridSizeX 27 PMEGridSizeY 27 PMEGridSizeZ 27 # WRAP WATER FOR OUTPUT wrapAll on # CONSTANT-T langevin on langevinTemp 300.0 langevinDamping 1.0 # CONSTANT-P LangevinPiston on LangevinPistonTarget 1 LangevinPistonPeriod 75 LangevinPistonDecay 25 LangevinPistonTemp 300 StrainRate 0.0 0.0 0.0 useGroupPressure yes # SPACE PARTITIONING splitpatch hydrogen hgroupcutoff 2.8 stepspercycle 10 margin 1.0 # CUT-OFFS switching on switchdist 9.0 cutoff 10.0 pairlistdist 11.0 limitDist 1.3 # RESPA fullElectFrequency 2 nonbondedFreq 1 # 1-4 NON-BONDED exclude scaled1-4 1-4scaling 1.0 # COM commotion no # SHAKE rigidbonds all rigidtolerance 0.000001 rigiditerations 400 # COLVARS SECTION colvars on colvarsConfig COMCOM.in # FEP PARAMETERS source /home/bits/Documents/FEP-tutorial-files/tools/fep.tcl alch on alchType FEP alchFile solvate.fep alchCol B alchOutFreq 10 alchOutFile forward.fepout alchElecLambdaStart 0.1 alchVdwLambdaEnd 1.0 alchVdwShiftCoeff 5.0 alchdecouple on alchEquilSteps 50 set numSteps 200 set dLambda 0.03125 runFEP 0.0 1.0 $dLambda $numSteps