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