#--- This is a test namd configuration file paratypeCharmm on parameters z.prm structure z.psf coordinates z_.pdb outputName z_2out set temperature 309 # temperature $temperature # continuing a run set inputname y_1restart binCoordinates $inputname.coor binVelocities $inputname.vel extendedSystem $inputname.xsc firsttimestep 2512500 # Integrator Parameters timestep 2 nonbondedFreq 1 fullElectFrequency 5 stepspercycle 10 rigidBonds all # Force-Field Parameters exclude scaled1-4 1-4scaling 0.8333333 cutoff 15 switching on switchdist 13 pairlistdist 17 # Constant Temperature Control nvt langevin on langevinDamping 1 langevinTemp $temperature langevinHydrogen off #--- PBC cellBasisVector1 47.0 0.0 0.0 cellBasisVector2 0.0 47.0 0.0 cellBasisVector3 0.0 0.0 300.0 #--- PME dielectric 1 PME on PMEGridSizeX 48 PMEGridSizeY 48 PMEGridSizeZ 300 #--- Output & Restart binaryoutput no binaryrestart yes restartname z_2restart DCDfile z_2out.dcd restartfreq 5000 dcdfreq 5000 xstFreq 5000 outputEnergies 5000 outputPressure 5000 outputtiming 5000 run 5000000 # 10 ns 1000 record