#Production NAMD config file for combinebox temperature 298.0 #coords structure and velocities structure combine.psf coordinates combine.coor #interactions paraTypeCharmm on parameters par_all27_prot_lipid.inp exclude scaled1-4 1-4scaling 1.0 switching on switchdist 10 cutoff 12 pairlistdist 13.5 stepspercycle 20 #next for shake rigidBonds water langevin on langevinTemp 298.0 langevinDamping 10.0 langevinHydrogen off # pressure control langevinPiston on langevinPistontarget 1.0 langevinPistonperiod 200 langevinPistondecay 100 langevinPistontemp 298 #pressure bath #next needed when shake'd useGroupPressure yes #kind of coupling #BerendsenPressure on #BerendsenPressureTarget 1.0 #BerendsenPressureCompressibility 0.00005 #BerendsenPressureRelaxationTime 200 #BerendsenPressureFreq 4 #use periodic boundary cellBasisVector1 31.4534 0.0 0.0 cellBasisVector2 0.0 31.4534 0.0 cellBasisVector3 0.0 0.0 31.4534 cellOrigin 0.0 0.0 0.0 wrapWater on #use PME PME on PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32 fullElectFrequency 4 #timing outputtiming 0 timestep 1.0 numsteps 960002 #output binaryoutput no outputname trajectory/tip3 outputEnergies 100 #save restart files binaryrestart no restartname trajectory/tip3 restartfreq 1000 restartsave yes # FEP fep on fepFile system.fep fepCol B fepOutFile system.fepout fepOutFreq 5 FepEquilSteps 3200 # LOOP OVER LAMBDA-STATES -- TCL set step 0.00 set dstep 0.01 while {$step <= 1.00} { firsttimestep 0 lambda $step set step [expr $step +$dstep] lambda2 $step run 6400 }