# Minimization of # 3d optimized in a 20 Water Box structure ../common/1EJG_wb.psf coordinates ../common/1EJG_wb.pdb binCoordinates ../run4/res.coor binVelocities ../run4/res.vel extendedSystem ../run4/res.xsc set temperature 300 set outputname 1EJG set restartname res firsttimestep 3039000 # Input paraTypeCharmm on parameters ../common/par_all27_prot_lipid.inp # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 rigidBonds all nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control langevin on langevinDamping 5 langevinTemp $temperature langevinHydrogen off ## Periodic Boundary Conditions cellBasisVector1 57.9 0. 0. cellBasisVector2 0. 53.7 0. cellBasisVector3 0. 0. 57.3 cellOrigin 11.2 10.0 6.3 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 60 PMEGridSizeY 54 PMEGridSizeZ 60 # Output outputName $outputname restartName $restartname outputEnergies 500 outputPressure 500 restartfreq 500 dcdfreq 500 xstFreq 500 # runs 0 time steps for each frame in the dcd # opens the dcd file to read the coordinates coorfile open dcd 1EJG-prot.dcd set i 0 while { ![coorfile read] } { incr i 500 firsttimestep $i run 0 } coorfile close