minimization of Vac Protein

mkMu_02mkVacMini.sh

#!/bin/sh
# GPL v. 3
# Program mkMu: 02mkVacMini.sh
# 
#
# written by Naoyuki Miyashita 7/22/2014
inputPrefix="01_dd"
outPrefix="02.min"

Temp=310
Size_x=98
Size_y=87
Size_z=85.8

PME_x=100
PME_y=90
PME_z=90
par="../../par/par_prot_wation.prm"
minfix="./02_min_fix.pdb"
program="perl set_pdb_constraint.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