#!/NAMD/namd2 # molecular system coordinates tssmssa_wb.pdb structure tssmssa_wb.psf #forcefield paratypecharmm on parameters par_all22_prot.inp exclude scaled1-4 1-4scaling 1.0 #for periodic boundary conditions cellBasisVector1 82.6 0.0 0.0 cellBasisVector2 0.0 81.7 0.0 cellBasisVector3 0.0 0.0 66.1 cellOrigin 1.52554261684 -0.995135366917 0.0983331128955 wrapAll on #PME settings PME on PMEGridSizeX 80 PMEGridSizeY 80 PMEGridSizeZ 66 #approximations switching on swtichdist 10 cutoff 12 pairlistdist 13.5 #integrator timestep 1.0 stepspercycle 20 nonbondedFreq 25 rigidBonds all fix protein #output outputenergies 10 outputtiming 100 binaryoutput no output tssmssa_min dcdfreq 100 #for restarting restartname tssmssa_min_restart restartfreq 500 restartsave yes binaryrestart yes temeperature 300 minimize 2000