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Chapter9.txt
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Chapter9.txt
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#PBS -N TrjconvAll
#PBS -j oe
#PBS -m e
#PBS -M [email protected]
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
set -vx
module load gromacs
>cd /fs/lustre/cwr0408/
>for l in EtOHMix50 EtOHMix00 EtOHMix70 EtOHMix100 EtOHMix80
>do
>cd /fs/lustre/cwr0408/$l
>for dir in */
>do
>cd /fs/lustre/cwr0408/$l/$dir
>echo 0 | trjconv -f md_concat.trr -s $l\_$dir\_EM.gro -o md_out.gro
>echo $dir | ./AnalyzeGro4
>done
>done
#PBS -N TrjCatConv+f+Dens
#PBS -j oe
#PBS -m e
#PBS -M [email protected]
#PBS -l walltime=12:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
>set -vx
>module load GROMACS/4.6.3
>cd /fs/lustre/cwr0408/
>for l in EtOHMix50 EtOHMix00 EtOHMix70 EtOHMix100 EtOHMix80
>do
>cd /fs/lustre/cwr0408/$l
?for dir in */
>do
>cd /fs/lustre/cwr0408/$l/$dir
>echo -e "0\n1000\n9000\n" | trjcat -settime -f firstmd.trr secondmd.trr thirdmd.trr -o md_concat.trr
>echo 0 | trjconv -f md_concat.trr -s $l\_${dir%?}\_EM.gro -o md_out.gro
>echo $dir | ./AnalyzeGro4
>echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_${i%?}\.xvg -dens mass -d Z
>echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_EtOH.xvg -dens mass -d Z
>echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_HOH.xvg -dens mass -d Z
>echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $l\_${dir%?}\_density_Sys.xvg -dens mass -d Z
>done
>done
#PBS -N TrjconvAll
#PBS -j oe
#PBS -m e
#PBS -M [email protected]
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
>set -vx
>module load GROMACS
>cd /fs/lustre/cwr0408/
>for l in EtOHMix50 EtOHMix00 EtOHMix70 EtOHMix100 EtOHMix80
>do
>cd /fs/lustre/cwr0408/$l
>for dir in */
>do
>cd /fs/lustre/cwr0408/$l/$dir
>echo 0 | trjconv -f md_concat.trr -s $l\_$dir\_EM.gro -o md_out.gro
>echo $dir | ./AnalyzeGro4
>done
>done
#PBS -N PE_10C_MS8ns
#PBS -j oe
#PBS -m abe
#PBS -M [email protected]
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
>set -vx
>module load GROMACS/4.6.3
>for l in EtOHMix00 EtOHMix50 EtOHMix70 EtOHMix80 EtOHMix100
>do
>for i in PE4 PE5 PE6 PE8 PE10 PE12 PE14 PE18 PE24 PP6 PP9 PP12 PP15 PP18 PIB12 PIB24 PIB36
>do
>cd /fs/lustre/cwr0408/$l/$i
>echo -e "6\n1" | g_rdf -f md_concat.trr -s md1.tpr -o $l\_$i\_rdf_HOH.xvg -com
>echo -e "6\n5" | g_rdf -f md_concat.trr -s md1.tpr -o $l\_$i\_rdf_$C\OH.xvg -com
>done
>done
>for l in EtOHMix00 EtOHMix50 EtOHMix70 EtOHMix80 EtOHMix100
>do
>module load GROMACS/4.6.3
>for i in PE4 PE5 PE6 PE8 PE10 PE12 PE14 PE18 PE24 PP6 PP9 PP12 PP15 PP18 PIB12 PIB24 PIB36
>do
>cd /fs/lustre/cwr0408/1.29.2014/$i
>echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_$i\.xvg -dens mass -symm -d Z
>echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_$C\OH.xvg -dens mass -symm -d Z
>echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_HOH.xvg -dens mass -symm -d Z
>echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_Sys.xvg -dens mass -symm -d Z
>done
>done
#This section of the code outputs many ensemble parameters.
>for l in EtOHMix00 EtOHMix50 EtOHMix70 EtOHMix80 EtOHMix100
>do
>for i in PE4 PE5 PE6 PE8 PE10 PE12 PE14 PE18 PE24 PP6 PP9 PP12 PP15 PP18 PIB12 PIB24 PIB36
>do
>cd /fs/lustre/cwr0408/$l/$i
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f firstmd.edr -s md1.tpr -o $l\_$i\_energy1.xvg
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f secondmd.edr -s md2.tpr -o $l\_$i\_energy2.xvg
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f thirdmd.edr -s md3.tpr -o $l\_$i\_energy3.xvg
>done
>done
>echo -e "0\n1000\n9000\n" | trjcat -settime -f firstmd.trr secondmd.trr thirdmd.trr -o md_concat.trr
>echo 0 | trjconv -f md_concat.trr -s $X\OHMix$C_$i_EM.gro -o md_out.gro
>echo $i | ./AnalyzeGro4
#Making the ndx file for Water ordering (only includes wa-ters)
>echo -e "name Water\nq" | make_ndx -f md_out.gro -o in-dex.ndx
#Making the GRO file for the calculation of the order param-eter
>echo 1 | trjconv -f md_concat.trr -s $X\_PP18_EM.gro -o md_out_order.gro
#May need to create a special GRO file with only water mole-cules (ndx required)
>echo 1 | g_order -f md_out_order.gro -s md1.tpr -o or-der.xvg
#Multiple RDF and density calls should be performed (density for each species and system [4] and mixture; rdf for each solvent [2])
#Computing the RDF of the polymer with water, then alcohol (no ndx needed)
>echo -e "6\n1" | g_rdf -f md_concat.trr -s md1.tpr -o $l\_$i\_rdf_HOH.xvg -com
>echo -e "6\n5" | g_rdf -f md_concat.trr -s md1.tpr -o $l\_$i\_rdf_$X\OH.xvg -com
>echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_$i.xvg -dens mass -d Z
>echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_$C\OH.xvg -dens mass -d Z
>echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_HOH.xvg -dens mass -d Z
>echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $l\_$i\_density_Sys.xvg -dens mass -d Z
It is required to plot and derive kD, the diffusion con-stant, from the mean squared displacement (MSD) separately, although it is given as a runtime output in the log. No ndx file required for MSD computations. These computations are only applied to the polymer or target molecule.
>echo 6 | g_msd -f md_concat.trr -s md1.tpr -o $l\_$i\_msd.xvg
>echo 6 | g_gyrate -f md_concat.trr -s md1.tpr -o $l\_$i\_gyrate.xvg
#Since the .EDR files are not concatenable, this is per-formed in three steps
#for plotting together in Excel or a similar program
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f firstmd.edr -s md1.tpr -o $l\_$i\_energy1.xvg
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f secondmd.edr -s md2.tpr -o $l\_$i\_energy2.xvg
>echo 2 3 4 5 6 7 8 12 33 34 35 36 23 27 31\n | g_energy -f thirdmd.edr -s md3.tpr -o $l\_$i\_energy3.xvg
Then add a section into the loop to copy each of these out-puts into some outputs folder:
>cp $l\_$i\_rdf_HOH.xvg $l\_$i\_rdf_$COH.xvg $l\_$i\_density_$i.xvg $l\_$i\_density_$COH.xvg /$l\outputs
>cp $l\_$i\_density_HOH.xvg $l\_$i\_density_Sys.xvg msd.xvg $l\_$i\_gyrate.xvg $l\_$i\_energy1.xvg /$l\outputs
>cp $l\_$i\_energy3.xvg $l\_$i\_energy3.xvg /$l/outputs
>cp r_concat.dat /$l/outputs/$l\_$i\_r.dat
>g_hbond -f md_concat.trr s- [].tpr -n index2.ndx -num hbnu-mixvg
where the ndx file is created first such that:
>make_ndx -f md_out.gro -o index.ndx
#PBS -N PE_4C_70MS1ns
#PBS -j oe
#PBS -m abe
#PBS -M [email protected]
#PBS -l walltime=1:59:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
>set -vx
>module load GROMACS/4.6.3
>cd $PBS_O_WORKDIR
>echo 1 2\n | g_hbond -f md_concat.trr -s md1.tpr -num hbnum.xvg
>#echo 1 5\n | g_hbond -f md_concat.trr -s md1.tpr -num hbnum2.xvg
>#echo 5 5\n | g_hbond -f md_concat.trr -s md1.tpr -num hbnum3.xvg
>#;echo 1 5\n | g_hbond -f md_out.gro -s md1.tpr -num hbnum.xvg
>echo 1 | g_h20order -f md_out.gro -s md1.tpr -o $X\OHMix$C\_$i\_order.xvg
>#echo 1 | g_order -f md_out_order.gro -s md1.tpr -o or-der.xvg
#PBS -N TRJCAT+f+dens
#PBS -j oe
#PBS -m abe
#PBS -M [email protected]
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=12
#PBS -S /bin/bash
>set -vx
#change the name of the folders
>module load GROMACS
>cd /fs/lustre/cwr0408/
>mv ./8.8.2013 ./EtOHMix50
>mv ./9.3.2013 ./EtOHMix00
>mv ./9.5.2013 ./EtOHMix70
>mv ./1.3.2014 ./EtOHMix100
>mv ./1.29.2014 ./EtOHMix80
>for l in EtOHMix50 EtOHMix00 EtOHMix70 EtOHMix100 EtOHMix80
>do
>cd /fs/lustre/cwr0408/$l
>for dir in */
>do
>cd /fs/lustre/cwr0408/$l/$dir
>echo $l $dir
>echo -e "0\n1000\n9000\n" | trjcat -settime -f firstmd.trr secondmd.trr thirdmd.trr -o md_concat.trr
#Running a pre-compiled Fortran program
>echo $dir | ./AnalyzeGro4
#Density computations
>echo -e "1" | g_density -f md_concat.trr -s md1.tpr -o $l_$dir_density_$i.xvg -dens mass -d Z
>echo -e "6" | g_density -f md_concat.trr -s md1.tpr -o $l_$dir_density_EtOH.xvg -dens mass -d Z
>echo -e "5" | g_density -f md_concat.trr -s md1.tpr -o $l_$dir_density_HOH.xvg -dens mass -d Z
>echo -e "0" | g_density -f md_concat.trr -s md1.tpr -o $l_$dir_density_Sys.xvg -dens mass -d Z
>done
>done
#change the name of the folders back
>mv ./EtOHMix50 ./8.8.2013
>mv ./EtOHMix00 ./9.3.2013
>mv ./EtOHMix70 ./9.5.2013
>mv ./EtOHMix100 ./1.3.2014
>mv ./EtOHMix80 ./1.29.2014
program Build
implicit none
integer MxN
parameter(MxN=27000)
real*8 xyz(3,MxN), dx(3), PL(3), drxy
real*8 R(MxN)
real*8 sum_nTop,sum_nBot, sum_nTot,sum_nMax
integer idum,ires, j, j2, k, Nat, iframe
integer nTop,nBot,nTot,iNotTop,iNotBot, ihit
character*3 tn
character*4 resID(MxN),resTarg
c.. MxN denotes the upper limit on the expected
c.. number of atoms in the system, which can be deter-mined from the
>c.. .gro file
c.. the input file is .gro file type
open(unit=39, file='md_out.gro', status='unknown')
c.. the output file is r2.dat
open(unit=49, file='r_concat.dat', status='unknown')
c.. read in 'the code' of the molecule you are analyzing
write(*,*) 'enter molecule type'
read(*,*) resTarg
sum_nTop=0.d0
sum_nBot=0.d0
sum_nTot=0.d0
sum_nMax=0.d0
c.. loop through the number of frames in the simulation (simulation-time-dependent var)
>do iframe =1,25000
c.. write out occasionally so you know where you are
if (mod(iframe,10).eq.0) write(*,*) iframe
c.. read a junk line, then the number of atoms
read(39,*) tn
read(39,*) Nat
c.. tn is the atom type
c.. Nat is the number of atoms
c.. loop through all atoms, j is a counting variable
do j=1,Nat
c.. read atom info: type of atom and position
read(39,129) ires, resID(j), tn, idum,
$ xyz(1,j),xyz(2,j),xyz(3,j)
>
c.. ires is
c.. resID is the atom number
c.. tn is
c.. set size of atom based on its type starting
c.. from the 13th column of the .gro file
R(j)=0.02d0
if (tn.eq.' OW'.or.tn.eq.' EO'.or.
$ tn.eq.' O'.or.tn.eq.
$ ' O'.or.tn.eq.'O') then
R(j)=.152
endif
if (tn.eq.'EC1'.or.tn.eq.'EC2'.or.
$ tn.eq.' C1'.or.tn.eq.' C2'.or.
$ tn.eq.'CH3'.or.tn.eq.' C'
$ .or.tn.eq.' C'.or.tn.eq.'C') then
> R(j)=.170
endif
if (tn.eq.' H'.or.tn.eq.' EH'.or.
$ tn.eq.'HW1'.or.tn.eq.'HW2'
$ .or.tn.eq.' H'.or.tn.eq.'H') then
R(j)=.120
endif
c.. this checks if an error and size not assigned
if (R(j).lt.0.03) then
write(*,*) 'xxxxx',j,tn
endif
enddo
c.. read junk line to get ready for next frame
read(39,130) PL(1),PL(2),PL(3)
nTop=0
nBot=0
nTot=0
c.. loop through all atoms; if its part of target mole-cule, proceed with analysis
do j=1,Nat
if (resID(j).eq.resTarg) then
iNotTop=0
iNotBot=0
c.. loop through all atoms; if NOT part of target mole-cule, proceed with analysis
do j2=1,Nat
if (resID(j2).ne.resTarg) then
c.. find distance in xy plane between atom in target mol-ecule and other atom
c.. apply periodic boundary conditions
do k=1,2
dx(k)=(xyz(k,j2)-xyz(k,j))
if(dabs(dx(k)+PL(k)).lt.dabs(dx(k)))dx(k)=dx(k)+PL(k)
if(dabs(dx(k)-PL(k)).lt.dabs(dx(k)))dx(k)=dx(k)-PL(k)
enddo
drxy= dsqrt( dx(1)**2 +dx(2)**2 )
c.. find distance in z direction between atom in target molecule and other atom
>c.. NO periodic boundary conditions
if(xyz(3,j2).gt.0.7*PL(3))xyz(3,j2)=xyz(3,j2)-PL(3)
dx(3)=(xyz(3,j2)-xyz(3,j))
c.. if distance in xy plane is less than sum of atom ra-dii -- then its an overlap
> ihit=0
if (drxy.lt.R(j)+R(j2)) ihit=1
c.. for overlaps, find out if atom in target molecule is on top or bottom
> if (ihit.eq.1) then
if (dx(3).gt.0.d0) then
iNotTop=1
else
iNotBot=1
endif
if (iNotTop.gt.0.and.iNotBot.gt.0) goto 10
endif
endif
enddo
if (iNotTop.eq.0) nTop=nTop+1
if (iNotBot.eq.0) nBot=nBot+1
10 continue
nTot=nTot+1
endif
enddo
c.. What do iNotTop and iNotBot represent?
c.. write(49,*) nTop, nBot, nTot
sum_nTop=sum_nTop +nTop
sum_nBot=sum_nBot +nBot
sum_nTot=sum_nTot +nTot
if (nTop.gt.nBot) then
sum_nMax=sum_nMax +nTop
else
sum_nMax=sum_nMax +nBot
endif
c.. nMax is 0 initially, but then it is
c.. nTop or nBot, whichever is greater
c.. for each frame, there are five digits written
c.. the first set goes to the screen and the second set goes
c.. to the r.dat file
c.. write(*,*) nTot
write(*,101) sum_nMax/sum_nTot,
$ sum_nTop/sum_nTot, sum_nBot/sum_nTot,
$ dble(nTop)/dble(nTot), dble(nBot)/dble(nTot)
>write(49,101) sum_nMax/sum_nTot,
$ sum_nTop/sum_nTot, sum_nBot/sum_nTot,
$ dble(nTop)/dble(nTot), dble(nBot)/dble(nTot)
>enddo
c.. the first number reported is nMax over the total num-ber
c.. the second number is nTop over the total number
c.. the third number is nBot over the total number
c.. the fourth number is double precision nTop over total
c.. the fifth number is double precision nBot over total
c.. These lines are telling the rest of the code about the form of the
>c.. inputs and outputs.
101 format(5f12.3)
129 format(i5,a4,3x,a3,i5,3f8.3)
130 format(3f10.3)
stop
end