# NAMD config file numsteps 500 structure pore+dna.psf coordinates pore+dna.pdb outputName eq1 XSTfile eq1.xst bincoordinates eq0.coor extendedSystem eq0.xsc temperature 0 reassignFreq 1 reassignTemp 0 reassignIncr 1 reassignHold 295 switching on switchDist 10 cutoff 12 pairlistdist 14 margin 3 binaryOutput yes binaryRestart yes parameters cornell.prm parameters par_silicon_ions_NEW5.inp paraTypeCharmm on wrapAll yes wrapNearest yes COMmotion no outputEnergies 100 outputTiming 100 xstFreq 100 dcdFreq 100 restartFreq 100 timestep 1 nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 Pme on PmeGridSizeX 48 PmeGridSizeY 48 PmeGridSizeZ 96 exclude scaled1-4 1-4scaling 1 constraints on consKCol B consref siliconRest_1.0.pdb consKFile siliconRest_1.0.pdb