############################################################# ## JOB DESCRIPTION ## ############################################################# # Eq. of KcsA # embedded in POPC membrane, ions and water. # Protein released. PME, Constant Pressure/Area. ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ref.psf coordinates ref.pdb set tcl_inp restrain2.tcl outputName PFT_prd_ns2 set temperature 300 # Continuing a job from the restart files if {1} { set inputname PFT_prd_ns1 binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem $inputname.restart.xsc } firsttimestep 500000 ############################################################# ## SIMULATION PARAMETERS##################################### ############################################################# #Input paraTypeCharmm on parameters par_all27_prot_lipid.prm #NOTE: Do not set the initial velocity temperature if you #have also specified a .vel restart file! #temperature $temperature #Periodic Boundary Conditions #NOTE: Do not set the periodic cell basis if you have also #specified an .xsc restart file! #if {0} { #cellBasisVector1 130. 0. 0. #cellBasisVector2 0. 134. 0. #cellBasisVector3 0. 0. 180. #cellOrigin 0.0 0.0 0.0 #} wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 10. switching on switchdist 8.5 pairlistdist 12.0 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 20 #PME (for full-system periodic electrostatics) if {1} { PME yes PMEGridSpacing 1.0 } # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature # Constant Pressure Control (variable volume) if {1} { useGroupPressure yes ;# needed for 2fs steps useFlexibleCell yes ;# no for water box, yes for membrane useConstantRatio yes ;# no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature } restartfreq 1000 ;# 1000steps = every 2ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 # Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on fixedAtomsFile nottails.fix.pdb fixedAtomsCol B fixedAtomsForces on } ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) #eFieldOn yes #eField 0 0 -0.155 ############################################################# ## EXECUTION SCRIPT ## ############################################################# tclForces on set targetAtomPdb ref_bb.pdb set forcesRecalcFreq 100 tclForcesScript $tcl_inp # Minimization if {0} { minimize 1000 reinitvels $temperature } run 500000 ;# 1.0 ns