Added the files and job script

build.sh

@@ -0,0 +1,121 @@
+#!/bin/bash
+
+BASE_DIR=`pwd`;
+BUILD_DIR="build"
+CPU=4
+#system info
+SOLVENT="octanol.pdb"
+TOT_SOLUTE=(pfmethanol.pdb pfethanol.pdb pfpropanol.pdb pfbutanol.pdb pfpentanol.pdb pfhexanol.pdb pfheptanol.pdb pfoctanol.pdb) 
+TOT_SOLUTE_RESNAME=(F3O F5O F7O F9O F11O F13O F15O F17O)
+#packing info
+N_SOLVENT=200
+BOX_SIZE=37.6
+#simulation info
+T=298
+P=1.01325
+RCUT=14
+RCUTLOW=0.01
+FE_MC=50000000 #steps for free energy simulation
+EQ_MC=2000000   #steps for eq simulation
+NPT_MC=10000000 #steps for NPT simulation
+FE_FREQ=5000    #free energy calc frequency
+STATES=(0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27)
+VDW=(0.0 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00)
+COUL=(0.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.20 0.40 0.60 0.70 0.80 0.90 1.00)
+
+
+
+if [ ${#COUL[@]} != ${#VDW[@]} ]; then 
+    echo "Warning: Number of Lambda states for VDW and COUL does not match!"
+    exit 1
+elif [ ${#STATES[@]} != ${#VDW[@]} ]; then
+    echo "Warning: Number of Lambda states for VDW and COUL does not match!"
+    exit 1
+fi
+if [ ${#SOLUTE[@]} != ${#SOLUTE_RESNAME[@]} ]; then 
+    echo "Warning: Number of solute and residue name are not same!"
+    exit 1
+fi
+
+for s in "${!TOT_SOLUTE[@]}"
+do
+    SOLUTE=${TOT_SOLUTE[s]}
+    SOLUTE_RESNAME=${TOT_SOLUTE_RESNAME[s]}
+    echo "Working on ${SOLUTE_RESNAME}"
+    WD=${BASE_DIR}/${SOLUTE_RESNAME}
+    mkdir $WD
+    cp -rf ${BASE_DIR}/${BUILD_DIR} $WD/.
+    cd $WD
+
+    echo "Packing the system for ${SOLUTE_RESNAME}"
+    cd ${BUILD_DIR}/pack/.
+    sed -i 's#SOLVENT#'${SOLVENT}'#g' Pack.inp;
+    sed -i 's#SOLV_NUM#'${N_SOLVENT}'#g' Pack.inp;
+    sed -i 's#SOLUTE#'${SOLUTE}'#g' Pack.inp;
+    sed -i 's#BOXSIZE#'${BOX_SIZE}'#g' Pack.inp;
+    ./packmol < Pack.inp >& PACK.log
+    vmd -dispdev text < build.tcl >& PACK.log
+
+    if [ ! -f "START.psf" ]; then
+	echo "Packing failed! Look at the ${WD}/${BUILD_DIR}/pack/PACK.log file."
+    fi
+
+    #set the common variable in config file
+    cd ${WD}/${BUILD_DIR}/input/.
+    sed -i 's#NCPU#'${CPU}'#g' *.sh
+    sed -i 's#TTT#'${T}'#g' *.conf
+    sed -i 's#PPPP#'${P}'#g' *.conf
+    sed -i 's#BOXSIZE#'${BOX_SIZE}'#g' *.conf
+    sed -i 's#RCUT#'${RCUT}'#g' *.conf
+    sed -i 's#RLOW#'${RCUTLOW}'#g' *.conf
+    sed -i 's#SOLUTE#'${SOLUTE_RESNAME}'#g' *.conf
+    sed -i s/"STATES"/"${STATES[*]}"/g *.conf
+    sed -i s/"LAMBDA_VDW"/"${VDW[*]}"/g *.conf
+    sed -i s/"LAMBDA_COULOMB"/"${COUL[*]}"/g *.conf
+
+
+    cd $WD
+    mkdir EQ
+    echo "Working on Equilibration files"
+    EQD=${WD}/EQ
+    cd ${EQD}
+    IND=${WD}/${BUILD_DIR}/input/
+    mkdir NVT NPT
+    EQ_JOB=${SOLUTE_RESNAME}"_eq.sh"
+    cp ${IND}/eq.sh ${EQ_JOB}
+    cp ${IND}/NVT.conf ./NVT/.
+    cp ${IND}/NPT.conf ./NPT/.
+    cp ${IND}/GOMC_CPU_NVT ./NVT/.
+    cp ${IND}/GOMC_CPU_NPT ./NPT/.
+    sed -i 's#RUN_DIR#'`pwd`'#g' ${EQ_JOB}
+    sed -i 's#MCSTEPS#'${EQ_MC}'#g' NVT/*.conf
+    sed -i 's#MCSTEPS#'${NPT_MC}'#g' NPT/*.conf
+    #qsub  ${EQ_JOB}
+
+    cd $WD
+    mkdir TI
+    echo "Working on Free Energy files: "
+    TID=${WD}/TI
+    cd ${TID}
+    N=$((${#VDW[@]}-1))
+    for d in $( seq 0 $N ); 
+    do 
+	DN="state_"$d
+	echo "    Building ${DN}"
+	PR_JOB=${SOLUTE_RESNAME}"_"$d".sh"
+	mkdir $DN
+	cd $DN
+	cp ${IND}/job.sh ${PR_JOB}
+	cp ${IND}/GOMC_CPU_NVT .
+	cp ${IND}/eq.conf .
+	cp ${IND}/prod.conf .
+	sed -i 's#MCSTEPS#'${EQ_MC}'#g' eq.conf
+	sed -i 's#MCSTEPS#'${FE_MC}'#g' prod.conf
+	sed -i 's#FREE_EN_FREQ#'${FE_FREQ}'#g' prod.conf
+	sed -i 's#RUN_DIR#'`pwd`'#g' ${PR_JOB}
+	sed -i 's#STATENUM#'${d}'#g' *.conf;
+	sed -i 's#INIT_STATE#'${d}'#g' *.conf
+	#qsub  ${PR_JOB}
+	cd ${TID}
+    done
+done

build/input/NPT.conf

@@ -0,0 +1,146 @@
+########################
+## Init File v2.0
+## 
+## IMPROVEMENTS
+## - Compacts inputs into one line
+## - Suggestion: edit inline with (insert key)
+##
+## To-Do 
+## (make editor + XML version)
+########################
+
+############################################################################
+#  ========-------------------- INPUT --------------------------===========
+############################################################################
+
+#########################
+# enable, step
+#########################
+Restart	 	true   
+
+####################################
+# kind {RESTART, RANDOM, INTSEED}
+####################################
+PRNG		RANDOM	
+
+####################################
+# FORCE FIELD
+####################################
+ParaTypeCHARMM	 true
+ParaTypeEXOTIC	 false
+Parameters     	 ../../build/model/parameter.par
+
+####################################
+# INPUT PDB FILES
+####################################
+Coordinates 0    ../NVT/EQ_NVT_BOX_0_restart.pdb
+
+####################################
+# INPUT PSF FILES
+####################################
+Structure  0 	 ../NVT/EQ_NVT_merged.psf
+
+############################################################################
+#  =======--------------------- SYSTEM --------------------------===========
+############################################################################
+
+##################################
+# GEMC TYPE (DEFULT IS NVT_GEMC)  
+##################################
+Pressure     PPPP
+
+#############################
+# SIMULATION CONDITION   
+#############################
+Temperature     TTT
+Potential       VDW 
+LRC		true
+Rcut		RCUT
+RcutLow         RLOW   
+Exclude 	1-4
+
+#############################
+# ELECTROSTATIC   
+#############################
+Ewald		true
+ElectroStatic   true
+Tolerance       0.00001
+1-4scaling      0.0
+CachedFourier   true
+
+###############################                                                
+# PRESSURE CALCULATION                                                   
+################################                                             
+PressureCalc   false
+
+################################
+# STEPS 
+################################
+RunSteps           MCSTEPS    
+EqSteps		   100000       
+AdjSteps	   10000        
+
+################################
+# MOVE FREQUENCY              
+################################
+DisFreq              0.48  
+RotFreq              0.20 
+RegrowthFreq         0.20
+CrankShaftFreq       0.10  
+VolFreq              0.02
+
+################################
+# FREE ENERGY PARAMETER
+################################
+FreeEnergyCalc true   MCSTEPS
+MoleculeType   SOLUTE   1
+InitialState   0   #no interaction for equilibration
+#states       STATES
+LambdaVDW     LAMBDA_VDW
+LambdaCoulomb LAMBDA_COULOMB
+
+
+################################
+# BOX DIMENSION #, X, Y, Z
+################################
+#CellBasisVector1  0  BOXSIZE 0.0 0.0
+#CellBasisVector2  0  0.0 BOXSIZE 0.0
+#CellBasisVector3  0  0.0 0.0 BOXSIZE
+
+
+##############################
+# CBMC TRIALS
+##############################
+CBMC_First   16     
+CBMC_Nth     8
+CBMC_Ang     100
+CBMC_Dih     100
+
+
+############################################################################
+#  =======-------------------- OUTPUT --------------------------===========
+############################################################################
+
+##########################
+# statistics filename add
+##########################
+OutputName  EQ_NPT
+
+#####################################
+# enable, frequency           
+#####################################
+CoordinatesFreq    true   100000
+RestartFreq  	   true   100000
+ConsoleFreq        true   100000
+BlockAverageFreq   true   100000
+
+
+##################################
+# enable: blk avg., fluct., 
+##################################
+OutEnergy         true    true    
+OutPressure       true    true      
+OutMolNum         true    true    
+OutVolume         true    true      
+OutDensity        true    true    
+