mirror of
https://github.com/nwchemgit/nwchem.git
synced 2026-07-28 14:15:30 -04:00
107 lines
2.3 KiB
Text
107 lines
2.3 KiB
Text
# This is a single NWChem input file which will start from a
|
|
# PDB format file and run a QM/MM calculation.
|
|
#
|
|
# Time steps and durations have been extended to better reflect
|
|
# what is necessary for better results. The workshop version
|
|
# had settings to make things complete faster.
|
|
|
|
Title "QM/MM Potassium Hexahydrate: Prep, Minimization, Dynamics."
|
|
|
|
memory noverify heap 8 mb stack 54 mb global 54 mb
|
|
|
|
start K6H2O
|
|
|
|
echo
|
|
|
|
# A basis set must be defined for the ESP charges on water
|
|
basis noprint
|
|
K library 6-31G*
|
|
H library 6-31G*
|
|
O library 6-31G*
|
|
end
|
|
|
|
# Assign segments for quantum mechanics region
|
|
# and solvate system. Maybe better done separately.
|
|
# Easiest way to do that is add the keyword 'stop'
|
|
# right after this prepare task.
|
|
prepare
|
|
system K6H2O_em
|
|
modify segment 1 quantum
|
|
#modify segment 2 quantum
|
|
#modify segment 3 quantum
|
|
#modify segment 4 quantum
|
|
#modify segment 5 quantum
|
|
#modify segment 6 quantum
|
|
#modify segment 7 quantum
|
|
center; orient
|
|
touch 0.23
|
|
expand 0.1
|
|
solvate
|
|
update lists
|
|
end; task prepare
|
|
|
|
# This is an optional step to write out the solvated system
|
|
# as a PDB file.
|
|
prepare
|
|
read K6H2O_em.rst
|
|
write pdb Kaq.pdb
|
|
end; task prepare
|
|
|
|
# A basis set must be defined for the QM part
|
|
basis noprint
|
|
K library sto-3g
|
|
H library sto-3g
|
|
O library sto-3g
|
|
end
|
|
|
|
# There is a net charge on the potassium ion.
|
|
charge 1.0
|
|
|
|
# Specify any SCF details
|
|
scf
|
|
print low geometry
|
|
end
|
|
|
|
# Define MM part of calculation for geometru optimization.
|
|
# ==> BE SURE TO SET MEMORY ASIDE FOR QM PART
|
|
md
|
|
system K6H2O_em
|
|
sd 50 init 0.01 min 0.00001 max 0.05
|
|
cg 30 init 0.01 min 1.0E-8 cy 10
|
|
cutoff 0.9 qmmm 0.5
|
|
memory 15000
|
|
end
|
|
|
|
# Define combined QM/MM part. Need to give quantum energy
|
|
# for atoms in atomic units (Hartrees).
|
|
qmmm
|
|
eatoms -1043.05
|
|
end
|
|
|
|
# Run QM/MM optimization.
|
|
task qmmm scf optimize
|
|
|
|
# Need to write out restart file for dynamics simulation.
|
|
# Optionally write out the current coordinates as PDB file.
|
|
prepare
|
|
read K6H2O_em.qrs
|
|
write Kaq_opt.pdb
|
|
write K6H2O_md.rst
|
|
end; task prepare
|
|
|
|
# Define changes to MM part for dynamics simulation.
|
|
md
|
|
system K6H2O_md
|
|
cutoff 0.9 qmmm 0.5
|
|
memory 15000
|
|
step 0.0005 equil 100 data 500
|
|
isotherm 300.0 trelax 0.1
|
|
print step 20 stat 100
|
|
record rest 10 coord 1
|
|
update pairs 2
|
|
end
|
|
|
|
# Run QM/MM dynamics.
|
|
task qmmm scf dynamics
|
|
|
|
|