############################################################# ## JOB DESCRIPTION ## ############################################################# # MD run of nAChR/POPC complex embedded in POPC # tethered protein, membrane, ions and water # # test of pulling ion through # # time-step = 2 fs, 310 K, pressure = 1 atm ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure nachr_popcwi.psf coordinates nachr_popcwi.pdb outputName dcdanalysis2 set temperature 310 # Continuing a job from the restart files if {1} { set inputname nachr_popcwi_ae032 binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel extendedSystem $inputname.restart.xsc } firsttimestep 20000000 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipidNBFIX.prm # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! #temperature $temperature # parallelisation parameters ldbUnloadZero yes twoAwayX no twoAwayY no twoAwayZ no # 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. 130. 0. cellBasisVector3 0. 0. 215. cellOrigin 0.03373091667890549 0.019359348341822624 7.807497501373291 } wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching off LJcorrection yes pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# in femtoseconds rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 1 stepspercycle 1 #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 500 dcdfreq 25 xstFreq 500 outputEnergies 500 outputPressure 500 set selfile selexample.pdb set selfmode on # Atoms in group 1 have 1s in the B column; those in group 2 have 0s. pairInteraction on pairInteractionFile $selfile pairInteractionSelf $selfmode pairInteractionCol B pairInteractionGroup1 1 pairInteractionGroup2 0 # pressure profile pressureProfile on pressureProfileSlabs 1 pressureProfileFreq 25 # First frame saved was frame 1000. set freq 25 set ts $freq coorfile open dcd nachr_popcwi_pi01.dcd # Read all frames until nonzero is returned. while { ![coorfile read] } { # Set firstTimestep so our energy output has the correct TS. firstTimestep $ts # Compute energies and forces, but don't try to move the atoms. run 0 incr ts $freq } coorfile close