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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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