AN INTRODUCTION TO
GAMESS
See: www.msg.chem.iastate.edu
GAMESS
•  General Atomic and Molecular Electronic
Structure System
•  General purpose electronic structure code
•  Primary focus is on ab initio quantum
chemistry calculations
•  Also can do
– Density functional theory calculations
– Other semi-empirical calculations (AM1, PM3)
– QM/MM calculations
REACTION PATHS
•  Reaction path is least energy path
– From reactants (R) through TS to products (P)
• Minimum energy path (MEP)
• Also called intrinsic reaction coordinate (IRC)
• Follows steepest descent path from TS to R or P
• Steepest descent means -gradient
– IRC = MEP:
• Confirms connection between R, TS, P
• Provides first step in study of reaction dynamics
CORRELATION METHODS
•  Perturbation theory
– E = E(0) + E(1) + E(2) + …
• Simplest E(0) = EHF: Then, E(1) = 0
• If series is terminated at second order: MP2
• Series does not always to converge well
– Best to just stop at MP2 (MP3, MP4 often terrible)
• MP2 scales as N5
– Often good compromise between efficiency & accuracy
• Includes dispersion naturally
• Often over-binds weak interactions (benzene dimer)
CORRELATION METHODS
•  Coupled cluster theory
– Ψ = eTΨ0
• Ψ0 usually is ΨHF
• T = cluster operator = T1+T2+T3+…+TN
• T1 = sum of 1-particle operators = ∑ti (N4 scaling)
• T2 = sum of 2-particle operators = ∑ ∑[tij+titj] (N6 scaling)
• T3 = sum of 3-particle operators = ∑ ∑ ∑[tijk+titjk+…] (N8)
• Approximations
• T≈T1 + T2: CCSD (singles (S) + doubles (D))
• T ≈T1 + T2 + T3: CCSDT (very expensive)
• Common compromise: CCSD(T): N7 scaling
– Get triples (T) using perturbation theory (not iterative)
OVERVIEW OF GAMESS
•  Types of wavefunctions
– Hartree-Fock (RHF, ROHF, UHF, GVB)
– CASSCF
– CI, MRCI
– Coupled cluster methods
– Second order perturbation theory
• MP2 (closed shells)
• ROMP2 (spin-correct open shells)
• UMP2 (unrestricted open shells
• MCQDPT(CASSCF - MRMP2)
– Localized orbitals (SCF, MCSCF)
OVERVIEW OF GAMESS
•  Types of wavefunctions
– Fragment Molecular Orbital Theory (FMO)
• Enables calculations on very large systems
– Thousands of atoms
• HF, DFT, MP2 (closed shells)
• ROMP2 (spin-correct open shells)
• Coupled Cluster methods
• MCSCF
OVERVIEW OF GAMESS
•  Energy-related properties
– Total energy as function of nuclear coordinates
(PES): All wavefunction types
– Analytic energy gradient
• RHF, ROHF, UHF, MCSCF, CI, DFT
• MP2, UMP2, ROMP2
– Analytic Hessian
• RHF, ROHF, TCSCF/GVB
• MCSCF
OVERVIEW OF GAMESS
•  Energy-related properties (cont’d)
– Numerical Hessians from finite differences of
analytic gradients
– Fully numerical derivatives for all methods
– Saddle point (TS) search (requires Hessian)
– Minimum energy path=Intrinsic reaction coordinate
• Several IRC options - GS2 (default) is most effective
• Requires frequency input, gradients along path
• Follow reaction path from reactants through TS to
products
• Build reaction path Hamiltonian (RPH): dynamics
OVERVIEW OF GAMESS
•  Energy-related properties (cont’d)
– Dynamic reaction coordinate (DRC)
• Add kinetic energy to system at any geometry
• Add photon(s) to any vibrational mode
• Classical trajectory using QM-derived energies
• Requires gradients
– Monte Carlo sampling: find global minimum
– Molecular dynamics
• MM only so far
OVERVIEW OF GAMESS
•  Other functionalities
– Spin-orbit coupling
• Any spin states, any number of states
• Full two-electron Breit-Pauli
• Partial two-electron (P2e)-very efficient, accurate
• Semi-empirical one-electron Zeff
• RESC
• Averaging over vibrational states
– Other relativistic effects: Douglas-Kroll to 3rd order
– Derivative (vibronic) coupling
• Only MCSCF at present
OVERVIEW OF GAMESS
•  Interpretive tools
– Localized molecular orbitals (LMO)
– Localized charge distributions (LCD)
– MCSCF localized orbitals
•  Nuclear and spectroscopic properties
– Spin densities at nucleus (ESR)
– NMR chemical shifts
– Polarizabilities, hyperpolarizabilities
– IR and Raman intensities
– Transition probabilities, Franck-Condon overlaps
OVERVIEW OF GAMESS
•  QM/MM Methods
– Effective fragment potential (EFP) method for
• Cluster studies of liquids
• Cluster studies of solvent effects
• Interfaced with continuum methods for study of liquids
and solvation in bulk
• Covalent link for study of enzymes, proteins, materials
• General model for intermolecular interactions
– SIMOMM: QM/MM method for surface chemistry
• QM part can be any method in GAMESS
• MM part from Tinker (Jay Ponder - Washington U)
• Moving to ReaxFF (Goddard)
USING GAMESS
•  GAMESS runs on
– Any UNIX-based system
– Any Linux-based system
– Any Macintosh
– Windows
•  GAMESS can be downloaded from
– www.msg.chem.iastate.edu
– License required - no cost
USING GAMESS
•  For Macintosh
– OSX, same as UNIX/LINUX
•  For UNIX/LINUX systems requires script
•  Output appears in .log file
•  Vectors, coordinates, Hessians in .dat file
•  IRC data, numerical restart data for frequencies
appear in .irc file
•  Main Monte Carlo output in .irc file
USING GAMESS
•  Input files are modular, arranged in $groups
•  Most common input groups
– $SYSTEM: specifies memory, time limit
– $CONTRL: specifies basics of calculation
– $BASIS: specifies basis set if standard
– $DATA: specifies nuclear coordinates, basis set if
non-standard
•  Other important groups:
– $GUESS, $SCF, $FORCE, $HESS, $VEC, $IRC,
$VIB
USING GAMESS
•  $ sign specifying group must be in column 2
•  All groups must terminate with $END (this $
can be anywhere except column 1)
USING GAMESS
•  $SYSTEM group:
– TIMLIM=(default=600 min)
– MWORDS=(default=1)
– MEMDDI=
• Only relevant for parallel run
• Total required memory (divide by number of
processors to get memory requested/node)
USING GAMESS
•  $CONTRL group:
– ICHARG= (specifies charge on system)
– MULT= (specifies spin multiplcity)
• 1 for singlet, 2 for doublet, …
– EXETYP=
• Check: checks input for errors
• Run: actual run
– UNITS=
• angs (default)
• bohr
USING GAMESS
•  $CONTRL group:
– Runtyp= (type of run)
• Energy (single point energy run)
• Gradient (energy 1st derivative wrt coordinates)
• Optimize (optimize geometry)
• Hessian (energy second derivative, vibrational
frequencies, thermodynamic properties):
generates $HESS group in .dat file)
• Sadpoint (saddle point search:requires hessian
in $HESS group)
• IRC (performs IRC calculation: usually requires
$IRC group, $HESS group)
USING GAMESS
•  $CONTRL group:
– scftyp= (type of wavefunction)
• RHF
• ROHF
• UHF
• MCSCF
• GVB
– mplevl=
• 0 (default, no perturbation theory)
• 2 (MP2: valid for RHF, ROHF, MCSCF, GVB)
– DFTTYP=
• None (default)
• xxx Specify name of functional
USING GAMESS
•  $CONTRL group:
– cctyp=
• NONE (no coupled cluster, default)
• CCSD (singles+doubles)
• CCSD(T) adds perturbative triples to CCSD
– Most popular method
– Triples essential for accurate calculations
• CR-CCL
– Specialized method to approximate bond-breaking
• EOM-CCSD, CR-EOM
– Excited states vi equaitons-of-motion CC
USING GAMESS
•  $BASIS group:
– GBASIS=
• STO
• N21
• N31
• TZV…
– NGAUSS=(# gaussians for STO, N21, N31)
– NDFUNC=(# sets of d’s on heavy atoms)
– NPFUNC=(# sets of p’s on hydrogens)
– NFFUNC=(# sets of f’s on TM’s)
USING GAMESS
•  $BASIS group:
– DIFFSP=.T. (diffuse sp functions on heavy atoms)
– DIFFS=.T. (diffuse s functions on hydrogens)
– GBASIS=ccn (correlation consistent)
• n=2,3,4,5,6
– GBASIS=accn (augmented cc--pVXZ)
– GBASIS=ccnc (core correlation)
– GBASIS=acnc (augmented core correlation)
– GBASIS=MC-DZP, MC-TZP, MC-QZP
•  basis set #bf #2-EI (theory) #2-EI (actual) CPU time (sec)
•  ccd 24 41,472 13863 .1
•  cct 58 1,414,562 566,091 .3
•  acct 92 8,954,912 3,754,821 1.4
•  ccq 115 21,862,578 11,695,586 4.0
•  accq 172 109,401,632 64,214,254 19.7
HF WATER
•  HF Scales ~ N4, n = # basis functions
•  (172/115)4 = 5.0: 19.7/4.0 = 4.9
USING GAMESS
•  $DATA group
– Title line (will be printed in output)
– Symmetry group
• C1
• CS
• CNV 2 (C2V), …
• Blank line except C1
USING GAMESS
•  $DATA group
– Symbol Z xcoord ycoord zcoord
• Symbol = atomic symbol
• Z = atomic number
• xcoord,ycoord, zcoord = Cartesian coords
• Internal coords is another option
– Repeat this line for each symmetry unique
atom (see below)
– Need to specify basis set after each
coordinate line if $BASIS is not present
USING GAMESS
•  $DATA group
– symmetry unique atoms
• H2O: O and 1 H
• NH3: N and 1 H
– saves CPU time
• numerical hessians only displace symmetry unique atoms
• Reduces # integrals to be calculated
– Need to follow conventions in GAMESS manual
• Cs, Cnh: plane is XY
• Cnv: axis is Z
– For Cinfv, use C4v
– For Dinfh, use D4h
USING GAMESS
•  $GUESS group
– Built-in guess (default) works much of the
time
– GUESS=MOREAD,NORB=xx $END
• Requires $VEC group (usually from .dat file)
• NORB=# MO’s to be read in
• Useful when SCF convergence is difficult
• Necessary for MCSCF, CI
RUNNING GAMESS
•  Prepare input file
– Within UNIX/Linux using vi line editor
– On Mac or PC using editor of choice
– Name of file must be xxx.inp
•  Submit job by
– gms xxx -q fred -l xxx.geomopt.log
RUNNING GAMESS
•  Output files
– .log file appears in directory in which job was
submitted
– .dat file contains basis set, coordinates,
orbitals ($VEC group), gradient ($grad
group),hessian ($HESS group), depending on
type of run
– .irc file contains $VIB group (restart for
numerical hessians), $IRC group
– Destroy .dat file & .irc file before re-running
• rm ~/scr/xxx.dat
• For more info, see
– www.msg.chem.iastate.edu
– GAMESS sub-page
RUNNING GAMESS