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| #!/bin/sh | |
| # GPL v. 3 | |
| # Program mkMu: 05mkVacMini.sh | |
| # | |
| # | |
| # written by Naoyuki Miyashita 7/22/2014 | |
| inputPrefix="04_ddng" | |
| outPrefix="05.min" | |
| Temp=310 | |
| c1=`grep -e size 04_ddng.dat | awk '{print $4}'` | |
| c2=`grep -e size 04_ddng.dat | awk '{print $5}'` | |
| c3=`grep -e size 04_ddng.dat | awk '{print $6}'` | |
| Size_x=$c1 | |
| Size_y=$c2 | |
| Size_z=$c3 | |
| PME_x=90 | |
| PME_y=81 | |
| PME_z=81 | |
| par="../../par/par_prot_wation.prm" | |
| minfix="./05_min_fix.pdb" | |
| program="perl set_minfix.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 20\n | |
| \n | |
| set tempe $Temp\n | |
| set outputname $outPrefix/r.$outPrefix\n | |
| #set inputname r_$outPrefix\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 none ;# needed for 2fs steps\n | |
| nonbondedFreq 1\n | |
| fullElectFrequency 2 \n | |
| stepspercycle 10\n | |
| longSplitting c2\n | |
| \n | |
| # Constant Temperature Control\n | |
| langevin off ;# 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 yes\n | |
| useConstantArea no \n | |
| useConstantRatio yes\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 03_min_fix2.pdb\n | |
| #conskfile 03_min_fix2.pdb\n | |
| #conskcol O\n | |
| #constraintScaling 1.0\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 on\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 5000000 ; # 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 |
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