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# Prepare the simulation
tleap -s -f input_create_complex.in # Creates HEM/CYS libs
ambpdb -p protein.prmtop < protein.inpcrd > solvated.pdb
if [ ! $? == 0 ]
then
echo "ERROR - System Preparation"
exit 1
fi
# Two stage energy minimization
ibrun pmemd.cuda -O -i min_sol.in -o min_sol.out -p protein.prmtop -c protein.inpcrd -r min_sol.rst -ref protein.inpcrd
ibrun pmemd.cuda -O -i min_all.in -o min_all.out -p protein.prmtop -c min_sol.rst -r min_all.rst -ref protein.inpcrd
if [ ! $? == 0 ]
then
echo "ERROR - System Minimization"
exit 2
fi
ambpdb -p protein.prmtop < min_all.rst > minimized.pdb
# Heat the system
ibrun pmemd.cuda.MPI -O -i heat.in -o heat.out -p protein.prmtop -c min_all.rst -r heat.rst -x heat.nc -ref min_all.rst
if [ ! $? == 0 ]
then
echo "ERROR - System Heating"
exit 3
fi
# Provide density
ibrun pmemd.cuda.MPI -O -i density.in -o density.out -p protein.prmtop -c heat.rst -r density.rst -x density.nc -ref min_all.rst
if [ ! $? == 0 ]
then
echo "ERROR - System Density"
exit 4
fi
# NVE Equilibirum for 1 ns
ibrun pmemd.cuda.MPI -O -i equil.in -o equil.out -p protein.prmtop -c density.rst -r equil.rst -x equil.nc -ref min_all.rst
if [ ! $? == 0 ]
then
echo "ERROR - NVE Equilibirum"
exit 5
fi
# Analyze Equilibirum simulation
mkdir analysis
cd analysis
perl ../process_mdout.perl ../heat.out ../density.out ../equil.out
exit # Remove this comment this out after first run
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