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DEPRECATED_LipidSys.sh
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DEPRECATED_LipidSys.sh
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#!/bin/bash
set -e
#export AMBERHOME=/home/thomas/amber18
#source $AMBERHOME/amber.sh
#Unpacked structure file:
#pdb=unpacked.pdb
## packmol-memgen --pdb ${pdb} --lipids DOPE:DOPG --ratio 3:1
pdbfilename=GakA.pdb
runname=GakA_mem
# Generate the lipid bilayer system:
packmol-memgen --pdb ${pdbfilename} --lipids DOPE:DOPG --ratio 3:1 --overwrite
## Calculate box size:
dims=$(./vmd_box_dims.sh -i bilayer_${pdbfilename} -s water)
## Generate AMBER input topology (prmtop) and input coordinates (inpcrd)
cat << EOF > system.in
source leaprc.protein.ff19SB
loadamberparams frcmod.ions1lm_126_iod_opc
source leaprc.water.opc
source leaprc.lipid17
system = loadpdb bilayer_${pdbfilename}
set system box { ${dims} }
saveamberparm system ${runname}.prmtop ${runname}.inpcrd
quit
EOF
tleap -f system.in
a=$(grep -n -m 1 "TER" bilayer_${pdbfilename} |cut -f1 -d:)
atomcount=$(expr $a - 3)
echo $atomcount
## minimization
cat <<EOF > min.in
Memgen AMBER minimization with restraints
&cntrl
nmropt = 0,
imin = 1,
maxcyc = 500,
ncyc = 250,
&end
EOF
## heat.in
cat <<EOF > heat.in
heat ${runname}
&cntrl
ig=-1
iwrap =1
imin=0,irest=0,ntx=1,
nstlim=2500,dt=0.001,
ntc=2,ntf=2,
cut=12, ntb=1, ntp=0,
ntpr=500, ntwx=500, ntwr=1000,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=300.0,
tol=1.0e-8,jfastw=0, nmropt=1,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
&wt TYPE='TEMP0', istep1=0, istep2=20000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
EOF
## prod.in
cat <<EOF > prod.in
equil ${runname}
&cntrl
ig=-1
iwrap =1
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
ntc=2,ntf=2,
cut=12, ntb=1, ntp=0, tautp=10.0,
ntpr=1000, ntwx=1000, ntwr=10000, ntwv=-1, ioutfm=1, ntwprt=$atomcount,
ntt=1,
temp0=300.0,
tol=1.0e-8,jfastw=0,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
EOF
date +"%T"
echo 'Production minimization'
mpirun -np 4 sander.MPI -O -i min.in -o minmdout -p ${runname}.prmtop -c ${runname}.inpcrd -r ${runname}_min.xyz -x ${runname}_min.nc
date +"%T"
echo 'Production heating'
mpirun -np 4 sander.MPI -O -i heat.in -o heatmdout -p ${runname}.prmtop -c ${runname}_min.xyz -r ${runname}_heat.xyz -x ${runname}_heat.nc
# Performs 100 us of production MD, writing 50 000 frames of trajectory in total over 20 runs.
date +"%T"
echo 'Production run 1'
pmemd.cuda -O -i prod.in -o prodmdout -p ${runname}.prmtop -c ${runname}_equil.xyz -r ${runname}_prod1.xyz -x ${runname}_prod1.nc
# Repeat
for j in {2..20}
do
date +"%T"
echo 'Production run' $j
pmemd.cuda -O -i prod.in -o prod"$j"mdout -p ${runname}.prmtop -c ${runname}_prod"$(($j-1))".xyz -r ${runname}_prod"$j".xyz -x ${runname}_prod"$j".nc
done
j=21
## final_prod.in, writes all molecules in the system to trajectory.
cat <<EOF > finalprod.in
equil ${runname}
&cntrl
ig=-1
iwrap =1
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
ntc=2,ntf=2,
cut=12, ntb=1, ntp=0, tautp=10.0,
ntpr=1000, ntwx=1000, ntwr=10000, ntwv=-1, ioutfm=1,
ntt=1,
temp0=300.0,
tol=1.0e-8,jfastw=0,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
EOF
## A final production run writing the entire system to trajectory.
pmemd.cuda -O -i finalprod.in -o prod"$j"mdout -p ${runname}.prmtop -c ${runname}_prod"$(($j-1))".xyz -r ${runname}_prod"$j".xyz -x ${runname}_prod"$j".nc