{\rtf1\ansi\ansicpg1254\deff0\deflang1055{\fonttbl{\f0\froman\fprq2\fcharset162{\*\fname Times New Roman;}Times New Roman TUR;}{\f1\fswiss\fprq2\fcharset162 Calibri;}{\f2\fswiss\fcharset162{\*\fname Arial;}Arial TUR;}} {\*\generator Msftedit 5.41.15.1515;}\viewkind4\uc1\pard\f0\fs20 #--- This is a test namd configuration file\fs24\par \fs20\~\fs24\par \fs20 paratypeCharmm\~ on\fs24\par \fs20 parameters\~ a.prm\fs24\par \fs20\~\fs24\par \fs20 structure\~\~\~\~\~\~\~\~\~\~\~\~\~ a.psf\fs24\par \fs20 coordinates\~\~\~\~\~\~\~\~\~\~\~ a_.pdb\fs24\par \fs20 outputName\~\~\~\~\~\~\~\~\~\~\~\~ a_out\fs24\par \fs20\~\fs24\par \fs20 set temperature\~\~\~ 300\fs24\par \fs20 temperature $temperature\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 firsttimestep\~\~\~\~\~ 0\fs24\par \fs20\~\fs24\par \fs20 # Integrator Parameters\fs24\par \fs20 timestep\~\~\~\~\~\~\~\~\~\~\~ 1\fs24\par \fs20 nonbondedFreq\~\~\~\~\~\~ 1\fs24\par \fs20 fullElectFrequency\~ 5\fs24\par \fs20 stepspercycle\~\~\~\~\~\~ 10\fs24\par \fs20 rigidBonds\~\~\~\~\~\~\~\~\~ water \fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 # Force-Field Parameters\fs24\par \fs20 exclude\~\~\~\~\~\~\~\~\~\~ scaled1-4\fs24\par \fs20 1-4scaling\~ 0.8333333\fs24\par \fs20 cutoff\~\~\~\~\~\~\~\~\~ 23\fs24\par \fs20 switching\~\~\~\~\~\~ on\fs24\par \fs20 switchdist\~\~\~\~\~ 21\fs24\par \fs20 pairlistdist\~\~\~ 28\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 # Constant Temperature Control nvt\fs24\par \fs20 langevin\~\~\~\~\~\~\~\~\~\~\~ on\~\~\~ \fs24\par \fs20 langevinDamping\~\~\~\~ 5\~\~\~\~ \fs24\par \fs20 langevinTemp\~\~\~\~ \~\~\~$temperature\fs24\par \fs20 langevinHydrogen\~\~\~ off\~\~\~ \fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 #--- PBC\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 cellBasisVector1\~ 47. 0.0\~ 0.0\fs24\par \fs20 cellBasisVector2\~ 0.0\~ 47.\~ 0.0\fs24\par \fs20 cellBasisVector3\~ 0.0\~ 0.0\~ 70.\fs24\par \fs20\~\fs24\par \fs20 #--- PME\fs24\par \fs20\~\fs24\par \fs20 dielectric\~\~\~\~\~ 1\fs24\par \fs20 PME\~\~\~\~\~\~\~\~\~\~\~\~ on\fs24\par \fs20 PMEGridSizeX\~\~\~ 50\fs24\par \fs20 PMEGridSizeY\~\~\~ 50\fs24\par \fs20 PMEGridSizeZ\~\~\~ 72\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 #--- Output & Restart\fs24\par \fs20\~\fs24\par \fs20 binaryoutput\~\~\~ no\fs24\par \fs20\~\fs24\par \fs20 binaryrestart\~\~ yes\fs24\par \fs20\~\fs24\par \fs20 restartname\~\~\~\~ a_outrestart\fs24\par \fs20 DCDfile\~\~\~\~\~\~\~\~ a_out.dcd\fs24\par \fs20\~\fs24\par \fs20\~\fs24\par \fs20 restartfreq\~\~\~\~\~\~\~ 250\fs24\par \fs20 dcdfreq\~\~\~\~\~\~\~\~\~\~\~ 250\fs24\par \fs20 xstFreq\~\~\~\~\~\~\~\~\~\~\~ 250\fs24\par \fs20 outputEnergies\~\~\~\~ 250\fs24\par \fs20 forceDCDfreq\~\~\~\~\~\~ 250\fs24\par \fs20 outputPressure\~\~\~\~ 250\fs24\par \fs20 outputtiming\~\~\~\~\~\~ 250\fs24\par \fs20\~\fs24\par \fs20 minimize 12500\fs24\par \fs20 reinitvels\~\~\~\~\~\~\~\~\~ $temperature\fs24\par \fs20\~\fs24\par \fs20 run 1000000\fs24\par \fs20\~\fs24\par \pard\sa200\sl276\slmult1\f1\fs22\par \pard\f2\fs20\par }