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yukimya/mkMu_06mkAllEqu.sh

Created July 22, 2014 08:35
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  1. yukimya created this gist Jul 22, 2014.
    194 changes: 194 additions & 0 deletions mkMu_06mkAllEqu.sh
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    #!/bin/sh
    # GPL v. 3
    # Program mkMu: 06mkAllEqu.sh
    #
    #
    # written by Naoyuki Miyashita 7/22/2014
    inputPrefix="04_ddng"
    inpPrefix="05.min"
    outPrefix="06.eq"

    scaling=10.0

    Temp=310
    Size_x=81.413
    Size_y=71.407
    Size_z=76.476

    PME_x=90
    PME_y=80
    PME_z=80
    par="../../par/par_prot_wation.prm"
    minfix="./06_min_fix2.pdb"
    program="perl set_minfix2.pl "

    nmpi=6

    mkdir $outPrefix

    line_0="
    #############################################################\n
    ## JOB DESCRIPTION ##\n
    #############################################################\n
    \n
    # Minimization\n
    \n
    #############################################################\n
    ## ADJUSTABLE PARAMETERS ##\n
    #############################################################\n
    set name $inputPrefix\n
    structure \$name.psf\n
    coordinates \$name.pdb\n
    set otime 2500\n
    set finalstep 50000
    \n
    set tempe $Temp\n
    set outputname $outPrefix/r.$outPrefix\n
    set inputname $inpPrefix/r.$inpPrefix\n
    \n
    binCoordinates \$inputname.restart.coor\n
    binVelocities \$inputname.restart.vel\n
    extendedSystem \$inputname.restart.xsc\n
    #\n
    # 7.11172 7.11172 8.81032\n
    #cellBasisVector1 $Size_x 0 0\n
    #cellBasisVector2 0 $Size_y 0\n
    #cellBasisVector3 0 0 $Size_z \n
    #cellOrigin 60.0 60.0 60.0\n
    #cellOrigin 0.0 0.0 0.0\n
    #6.74252 6.74252 9.81649\n
    #firsttimestep 2000\n
    \n
    #############################################################\n
    ## SIMULATION PARAMETERS ##\n
    #############################################################\n
    \n
    # Input\n
    paraTypeCharmm on\n
    parameters $par\n
    #parameters par_all36_lipid.prm\n
    #temperature \$tempe\n
    \n
    \n
    # Force-Field Parameters\n
    exclude scaled1-4\n
    1-4scaling 1.0\n
    cutoff 12.0\n
    switching on\n
    switchdist 10.0\n
    pairlistdist 14.0\n
    vdwForceSwitching off\n
    LJcorrection off\n
    \n
    # Integrator Parameters\n
    timestep 2.0 ;# 2fs/step\n
    rigidBonds all ;# needed for 2fs steps\n
    nonbondedFreq 1\n
    fullElectFrequency 2 \n
    stepspercycle 10\n
    longSplitting c2\n
    \n
    # Constant Temperature Control\n
    langevin on ;# do langevin dynamics\n
    langevinDamping 5 ;# damping coefficient (gamma) of 5/ps\n
    langevinTemp \$tempe\n
    langevinHydrogen off ;# don't couple langevin bath to hydrogens\n
    \n
    # Periodic Boundary Conditions\n
    \n
    wrapAll on\n
    wrapWater on\n
    wrapNearest on\n
    dcdUnitCell yes\n
    \n
    # PME (for full-system periodic electrostatics)\n
    PME yes\n
    PMEGridSizeX $PME_x\n
    PMEGridSizeY $PME_y\n
    PMEGridSizeZ $PME_z\n
    PMEGridSpacing 1.0\n
    margin 5.0\n
    \n
    # Constant Pressure Control\n
    useGroupPressure yes ; # needed for rigidBonds\n
    useFlexibleCell no\n
    useConstantArea no \n
    useConstantRatio no\n
    \n
    langevinPiston off\n
    langevinPistonTarget 1.01325 ; # in bar -> 1 atm \n
    langevinPistonPeriod 100.0\n
    langevinPistonDecay 50.0\n
    langevinPistonTemp \$tempe\n
    \n
    # Output\n
    outputName \$outputname\n
    \n
    restartfreq \$otime ;# 2500steps = every 5ps\n
    dcdfreq \$otime\n
    xstFreq \$otime\n
    outputEnergies \$otime\n
    outputPressure \$otime\n
    \n
    \n
    #############################################################\n
    ## EXTRA PARAMETERS ##\n
    #############################################################\n
    \n
    # Harmonic constraint\n
    constraints on\n
    consref $minfix\n
    conskfile $minfix\n
    conskcol O\n
    constraintScaling $scaling\n
    #\n
    # FIXED ATOM\n
    #fixedAtomsForces on\n
    #fixedAtoms on\n
    #fixedAtomsCol O\n
    #fixedAtomsFile $minfix\n
    \n
    #############################################################\n
    ## EXECUTION SCRIPT ##\n
    #############################################################\n
    \n
    # Minimization\n
    minimization off\n
    #minimize 10000\n
    #minimization on\n
    #minTinyStep 1.0e-11 # d 1.0e-6\n
    #minBabyStep 1.0e-7 # d 1.0e-2\n
    #minLineGoal 1.0e-9 # d 1.0e-4\n
    #minimize 10000\n
    \n
    #minimization on\n
    #minTinyStep 1.0e-8 # d 1.0e-6\n
    #minBabyStep 1.0e-5 # d 1.0e-2\n
    #minLineGoal 1.0e-7 # d 1.0e-4\n
    #minimize 2000\n
    \n
    #minimization on\n
    #minTinyStep 1.0e-6 # d 1.0e-6\n
    #minBabyStep 1.0e-3 # d 1.0e-2\n
    #minLineGoal 1.0e-5 # d 1.0e-4\n
    #minimize 1000\n
    \n
    #reinitvels \$temperature\n
    \n
    run \$finalstep ; # 10.0ns \n
    "
    echo -n -e $line_0 > $outPrefix.inp

    line_0="
    #!/bin/bash -f\n
    #$ -N $outPrefix\n
    #$ -V -S /bin/bash\n
    #$ -l gpu=1\n
    #$ -cwd\n
    namd2 +p$nmpi +idlepoll $outPrefix.inp > $outPrefix/$outPrefix.out \n
    "
    echo -n -e $line_0 > $outPrefix.sh

    # run
    $program $inputPrefix.pdb > $minfix
    sh $outPrefix.sh