# NAMD config file numsteps 15000 structure fu.psf coordinates fu.pdb outputName eq2 XSTfile eq2.xst bincoordinates eq1.coor binvelocities eq1.vel extendedSystem eq1.xsc langevin off langevinDamping 3 langevinTemp 310 langevinHydrogen on switching on switchDist 10 cutoff 12 pairlistdist 14 margin 3 binaryOutput yes binaryRestart yes parameters par file.par parameters par2.prm paraTypeCharmm on wrapAll yes wrapNearest yes COMmotion no outputEnergies 500 outputTiming 500 xstFreq 500 dcdFreq 250 restartFreq 500 timestep 1 nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 Pme off PmeGridSizeX 40 PmeGridSizeY 40 PmeGridSizeZ 40 exclude scaled1-4 1-4scaling 1 alch on alchType FEP alchFile fu.fep alchCol B alchOutFile forward-off.fepout alchOutFreq 5 set numSteps 500 alchDecouple off set Lambda0 0.0 set dLambda 0.1 while {$Lambda0 <= 1.0} { alchLambda $Lambda0 set Lambda0 [expr \$Lambda0 + \$dLambda] alchLambda2 $Lambda0 run 10000 }