############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Collagen domain in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ionized.psf coordinates ionized.pdb set temperature 310 set outputname ionized_eq firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../toppar/par_all36m_prot.prm parameters ../toppar/par_all36_na.prm parameters ../toppar/par_all36_carb.prm parameters ../toppar/par_all36_lipid.prm parameters ../toppar/par_all36_cgenff.prm parameters ../toppar/par_interface.prm parameters ../toppar/toppar_all36_nano_lig.str parameters ../toppar/toppar_all36_nanolig_patch.str parameters ../toppar/toppar_water_ions.str parameters ../toppar/toppar_ions_won.str parameters ../toppar/toppar_all36_prot_c36m_d_aminoacids.str parameters ../toppar/toppar_all36_prot_na_combined.str parameters ../toppar/toppar_all36_prot_modify_res.str parameters ../toppar/toppar_all36_na_nad_ppi.str temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 pairlistsPerCycle 2 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 1/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary conditions. Need this since for a start... cellBasisVector1 238.5 0.0 0.0; # vector to the next image cellBasisVector2 0.0 44.8 0.0; cellBasisVector3 0.0 0.0 45.8; cellOrigin 107.8 2.6 2.5; # the *center* of the cell wrapWater on; # wrap water to central cell wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEInterpOrder 6; # interpolation order (spline order 6 in charmm) PMEGridSpacing 1.0 #manual grid definition #PMEGridSizeX 250 #PMEGridSizeY 55 #PMEGridSizeZ 55 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100.0 langevinPistonDecay 50.0 langevinPistonTemp $temperature # Output outputName $outputname restartfreq 5000; # 5000 steps = every 10ps dcdfreq 50000; dcdUnitCell yes; # the file will contain unit cell info in the style of # charmm dcd files. if yes, the dcd files will contain # unit cell information in the style of charmm DCD files. xstFreq 5000; # XSTFreq: control how often the extended systen configuration # will be appended to the XST file outputEnergies 5000; # 5000 steps = every 10ps # The number of timesteps between each energy output of NAMD outputTiming 1000; # The number of timesteps between each timing output shows # time per step and time to completion ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 10000 reinitvels $temperature run 5000000; # 10ns