Young - Computational chemistry

A.2 AB INITIO AND DFT SOFTWARE 337

tered in modeling inorganic systems. Nonetheless, inorganic modeling generally requires additional technical sophistication on the part of the user.

Gaussian is designed to execute as a batch job. It can readily be used with common batch-queueing systems. The program may be purchased as source code or executables and comes with hundreds of sample input and output ®les. These may be employed as examples of how to construct inputs. They may also be employed to verify that a compilation from source code was successful. In our experience, such veri®cation is essential.

Price category: production, departmental, institutional

Platforms: PC (Windows and Linux), DEC, Cray, Fujitsu, HP-UX, RS/ 6000, NEC, SGI, Sun

Contact information: Gaussian, Inc. Carnegie O½ce Park, Bldg. 6 Suite 230

Pittsburgh, PA 15106 [phone] http://www.gaussian.com/ [e-mail]

A.2.5 Jaguar

Jaguar (we tested Version 3.5) is an ab initio program designed to e½ciently run calculations on large molecules. This is achieved through the developers' choice of algorithms and optimization strategy. Jaguar can use a pseudospectral integration scheme, which gives time complexities of N 3 or better for HF, GVB, DFT, and MP2 calculations. Performance increases are also obtained from the ability to use non-Abelian symmetry groups. Jaguar was formerly called PS-GVB.

The HF, GVB, local MP2, and DFT methods are available, as well as local, gradient-corrected, and hybrid density functionals. The GVB-RCI (restricted con®guration interaction) method is available to give correlation and correct bond dissociation with a minimum amount of CPU time. There is also a GVBDFT calculation available, which is a GVB-SCF calculation with a post-SCF DFT calculation. In addition, GVB-MP2 calculations are possible. Geometry optimizations can be performed with constraints. Both quasi-Newton and QST transition structure ®nding algorithms are available, as well as the SCRF solvation method.

The properties available include electrostatic charges, multipoles, polarizabilities, hyperpolarizabilities, and several population analysis schemes. Frequency correction factors can be applied automatically to computed vibrational frequencies. IR intensities may be computed along with frequency calculations.

Jaguar comes with a graphic user interface, but it is not a molecule builder. The interface can be used to set the program options. The user must input the geometry by typing in Cartesian coordinates or a Z-matrix. The interface may

338 APPENDIX A SOFTWARE PACKAGES

then be employed to import geometry information from a large list of ®le formats. Both geometry and calculation setup information can be imported from GAMESS, Gaussian, and Spartan ®les. Jaguar may also symmetrize a molecule if the coordinates do not exactly match a given point group. The online help is fairly detailed. When the calculation is executed, a separate window displays messages showing which step of the calculation is being executed.

At the time of this review, a new graphic user interface was under development. Jaguar can also be purchased as part of the Titan program, which combines Jaguar with the Spartan graphic interface. An orbital viewer for Jaguar is available from Serena Software.

Alternatively, the user can construct ASCII input ®les manually. The ®le format includes many numerical ¯ags to control the type of calculation. The researcher should plan on investing some time in learning to use the program in this way. Jaguar can be executed from the command line, making it possible to use batch processing or job queue systems.

For many researchers, Jaguar is the code of choice for running GVB or MP2 calculations on large molecules. For DFT calculations, there are two algorithms designed for e½ciency in modeling large molecules. One is the pseudospectral method in Jaguar and the other is the fast multipole method, which has been incorporated in the Gaussian 98 and Q-Chem packages. Our reviewer ran identical calculations on several large molecules with all three packages. For some molecules, all three packages used nearly exactly the same amount of CPU time. For one test, Jaguar was 43% faster than the others. And for one test, Jaguar was 49% slower. Our reviewer was not able to propose any speci®c criteria for predicting which molecules would run faster or slower with each package. One published study shows Jaguar giving as much as a 25-fold speed advantage over Gaussian 92 [R. A. Friesner, R. B. Murphy, M. D. Beachy, M. N. Ringnalda, W. T. Pollard, B. D. Dunietz, and Y. Cao (1999). J. Phys. Chem. A103, 1913.].

Price category: production and higher

Platforms: SGI, RS/6000, HP-UX, Cray, Alpha, PC (Linux only) Contact information: SchroÈdinger, Inc.

17 She½eld Drive West Grove, PA 19390 [phone]

http://www.schrodinger.com/

[e-mail]

A.2.6 MOLPRO

MOLPRO (we tested Version 98.1) is an ab initio program designed for performing complex calculations. This program is often used for calculations that present technical di½culties or are very sensitive to electron correlation. A few portions of the code have been parallelized.

A.2 AB INITIO AND DFT SOFTWARE 339

Calculations that can be performed are HF, CI, MRCI, FCI, CC, DFT, MCSCF, CASSCF, ACPF, CEPA, valence bond, and many variations of these. Perturbation theory calculations can be done from singleand multipledeterminant references spaces. The MCSCF and coupled-cluster algorithms have proven to be very e½cient. Restricted, unrestricted, and restricted openshell wave functions are available. The user has a large amount of detailed control over wave function construction. Many one-electron properties can be computed, including relativistic energy corrections, spin-orbit coupling, electric ®eld gradients, and multipoles. A number of options for electronic excited states and transition-structure calculations are also available. It can use Gaussian basis sets with high-angular-momentum functions (spdfghi) and e¨ective core potentials.

The ASCII input ®le includes elements of a scripting language. Thus, the input can contain variables, loops, and procedures. This is one of the aspects of the program that makes it possible to do very complex calculations. The documentation describes the input options, but does not discuss when and why they should be used. The user must have a solid understanding of ab initio theory in order to correctly utilize many of the functions in this program. It is very powerful, but not for beginners.

The program uses dynamic memory allocation within a memory limit that must be set manually if the default is insu½cient. The program does store data in scratch ®les, but the size of these ®les has been kept to a minimum. The output is neatly formatted, but designed for wide carriage printers.

This program is excellent for high-accuracy and sophisticated ab initio calculations. It is ideal for technically di½cult problems, such as electronic excited states, open-shell systems, transition metals, and relativistic corrections. It is a good program if the user is willing to learn to use the more sophisticated ab initio techniques.

Price category: production, departmental, institutional

Platforms: Linux, Alpha, Cray, Fujitsu, AIX, SGI, Sun, HP-UX, NEC Contact information: P. J. Knowles

School of Chemistry University of Birmingham

Edgbaston, Birmingham, B15 2TT United Kingdom

‡44-121-414-7472 http://www.tc.bham.ac.uk/molpro/ [e-mail]

A.2.7 Q-Chem

Q-Chem (we tested Version 1.2) is an ab intio program designed for e½cient calculations on large molecules. Q-Chem uses ASCII input and output ®les.

340 APPENDIX A SOFTWARE PACKAGES

The HyperChem program from Hypercube Inc. and UniChem from Oxford Molecular can be used as graphic interfaces to Q-Chem. At the time we conducted our tests, it was not yet available on all the platforms listed as being supported. The current version is well designed for groundand excited-state calculations on small or large organic molecules.

Q-Chem includes HF, ROHF, UHF, and MP2 Hamiltonians as well as a good selection of DFT functionals. Mulliken and NBO population analysis methods are available. Multiple options are available for SCF convergence, geometry optimization, and initial guess. IR and Raman intensities can also be computed. In addition, the documentation was well written.

One of the major selling points of Q-Chem is its use of a continuous fast multipole method (CFMM) for linear scaling DFT calculations. Our tests comparing Gaussian FMM and Q-Chem CFMM indicated some calculations where Gaussian used less CPU time by as much as 6% and other cases where Q-Chem ran faster by as much as 43%. Q-Chem also required more memory to run. Both direct and semidirect integral evaluation routines are available in Q-Chem.

Gaussian users will ®nd that Q-Chem feels familiar. The ASCII input format is a bit more wordy than Gaussian; it is more similar to GAMESS input. The output is very similar to Gaussian output, but a bit cleaner. The code can easily be used with a job-queueing system.

Q-Chem also has a number of methods for electronic excited-state calculations, such as CIS, RPA, XCIS, and CIS(D). It also includes attachment± detachment analysis of excited-state wave functions. The program was robust for both single point and geometry optimized excited-state calculations that we tried.

Price category: production, departmental, institutional

Platforms: PC (Windows and Linux), DEC, Cray, Fujitsu, RS/6000, SP2, SGI, Sun

Contact information: Q-Chem, Inc. Four Triangle Drive

Suite 160

Export, PA 15632-9255 [phone] http://www.q-chem.com/ [e-mail]

A.3 SEMIEMPIRICAL SOFTWARE

Three popular semiempirical programs, AMPAC, AMSOL, and MOPAC, are actually derivations of the same original code. AMPAC 1.0 and MOPAC 3.0 were both created from Version 2.0 of MOPAC. AMSOL was derived from

A.3 SEMIEMPIRICAL SOFTWARE

341

Version 2.1 of AMPAC. All three of these programs have similar input and output ®les, but have been developed for di¨erent purposes. New additions to AMSOL have been almost exclusively methods for including solvent e¨ects. AMPAC was designed for e½cient operation on vector computers and for ®nding and testing transition structures. AMPAC is also the only one incorporating the SAM1 method. MOPAC is designed to be robust and to compute a large number of molecular properties, including algorithms for large-molecule calculations.

There are also semiempirical programs bundled with the Unichem, Spartan, and Hyperchem products discussed previously in this appendix.

A.3.1 AMPAC

AMPAC (we tested Version 6.51) is a semiempirical program. It comes with a graphic user interface (we tested Version 6.0). The documentation included with the package is well written.

The graphic interface has a molecule builder that is very easy to use. This is the same GUI as the GaussView interface from Gaussian Inc., that was licensed from Semichem. The one sold with AMPAC has screens for setting up and running AMPAC calculations. It can also be used to set up and analyze Gaussian 94 calculations, but the interface is not identical to the one in GaussView 1.0. The GUI is integrated well with the computational portion. See the GaussView description for more information on the GUI.

AMPAC can also be run from a shell or queue system using an ASCII input ®le. The input ®le format is easy to use. It consists of a molecular structure de®ned either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints.

AMPAC supports a number of semiempirical methods: AM1, SAM1, SAM1/d, MNDO, MNDO/d, MNDOC, MINDO/3, and PM3. The solvation methods available are SM1-SM3 and COSMO. Types of calculation available include single-point energies, geometry optimization, frequency calculation, IRC, and a reaction path and an annealing algorithm. It incorporates some transition structure ®nding algorithms that are not in other semiempirical programs, such as the CHAIN and TRUST algorithms. A simulated annealing algorithm is available for conformation searching. The code incorporates many alternative algorithms and settings to control how the calculation is performed. Property prediction functions include ESR and nonlinear optical properties.

Price category: production, departmental, institutional

Platforms: PC (Windows & Linux), SGI, RS6000, Alpha, Sun, HP-UX Contact information: Semichem

P.O. Box 1649

Shawnee Mission, KS 66222

342APPENDIX A SOFTWARE PACKAGES

[phone] http://www.semichem.com/ [e-mail]

A.3.2 MOPAC

MOPAC (we tested Versions 6 and 2000) stands for molecular orbital package. It is one of the most widely used semiempirical software packages and is designed for robustness and a wide range of functionality. Programs that can be used as a graphic interface for MOPAC are WinMOPAC from Fujitsu, Alchemy from SciVision, PC Model from Serena Software, Chem3D from CambridgeSoft, and HyperChem from HyperCube Inc.

The earlier versions of MOPAC were available at little or no cost. Many graphic interface programs are shipped with MOPAC, usually Version 6, which was the last free version. MOPAC 7 is a free beta version of the MOPAC 93 commercial code. MOPAC 6 is often preferred over Version 7 because of known bugs in Version 7. Older versions of MOPAC have also been incorporated into the Gaussian, Cache, and GAMESS programs. Since free versions of MOPAC have been bundled and sometimes modi®ed by commercial companies, some variations exist. These are most often di¨erences in the size of molecules that can be modeled. Slight di¨erences in performance and input format can also be found. The newest versions of MOPAC were developed by Fujitsu and marketed in North America by SchroÈdinger, Inc.

MOPAC runs in batch mode using an ASCII input ®le. The input ®le format is easy to use. It consists of a molecular structure de®ned either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. Version 6 and older have limits on the size of molecule that can be computed due to the use of ®xed array sizes, which can be changed by recompiling the source code. This input format allows MOPAC to be run in conjunction with a batch job-queueing system.

The MNDO, MINDO/3, AM1, and PM3 Hamiltonians are supported. Semiempirical calculations can be performed on high-spin systems and excited states using con®guration interaction. Transition structures and intrinsic reaction coordinates can be computed, as well as vibrational modes including the transition dipole. The program includes the ability to perform a computation with periodic boundary conditions in one, two, and three dimensions for modeling polymers, layer systems, and solids. Hyper®ne coupling constants and static and frequency-dependent hyperpolarizabilities can also be computed. In addition, a set of population analysis functions is available. Classical dynamics simulations on the semiempirical potential energy surface can also be performed.

MOPAC 2000 is the most recent commercial version of MOPAC. It includes improvements in a number of areas. The MNDO/d and AM1-d Hamiltonians are also now available. The program uses dynamic memory allocation. This results in calculations requiring less memory for small molecules and at the

A.3 SEMIEMPIRICAL SOFTWARE

343

same time accommodates exteremely large molecules. It also has improved algorithms for computations on very large biomolecules, which include faster calculations and determination of the net charge. The program additionally includes algorithms for modeling excited states in solution using the COSMO and Tomasi methods. It is possible to ®nd the geometry at which intersystem crossing is most likely to occur. The manual has been expanded to include a section addressing the accuracy of semiempirical calculations.

A semiempirical crystal band structure program, called BZ, is bundled with MOPAC 2000. There is also a utility, referred to as MAKPOL, for generating the input for band structure calculations with BZ. With the use of MAKPOL, the input for band-structure computations is only slightly more complicated than that for molecular calculations.

Price category: free (older versions), production, departmental, bundled with other programs

Platforms: PC, many UNIX systems Contact information: SchroÈdinger, Inc.

17 She½eld Drive West Grove, PA 19390 [phone]

http://www.schrodinger.com/

[e-mail]

A.3.3 YAeHMOP

YAeHMOP stands for yet another extended HuÈckel molecular orbital package. The package has two main executables and a number of associated utilities. The ``bind'' program does molecular and crystal band structure extended HuÈckel calculations. The ``viewkel'' program is used for displaying results. We tested Version 3.0 of bind and Version 2.0 of viewkel.

The bind program requires an ASCII input and generates one or more ASCII output ®les. The molecular geometry can be de®ned as a Z-matrix, Cartesian coordinates, or fractional coordinates. Periodic boundary condition calculations may be done in one, two, or three dimensions. The program has built-in parameters to describe most elements, although it is also possible to enter parameters manually. There is an automated function to generate the data for Walsh diagrams. Orbital occupations can be set manually in order to give electronic excited-state calculations. The program does not have an automated function for optimizing the molecular or unit cell geometry. The user must enter a list of k points and their weights in order to perform average property calculations. Information that can be computed includes the band structure, DOS, COOP, fragment molecular and crystal orbital analysis, MOs, Fermi energy, and Mulliken population analysis.

344 APPENDIX A SOFTWARE PACKAGES

The viewkel program allows the graphic display of results. It is not a graphic molecular structure builder and does not require any graphic display libraries other than those included in X-windows. It uses line-drawn graphics and can shade atoms by element. The program can also be used to display molecular and crystal structures, orbital isosurfaces, Walsh diagrams, and various plots of the band structure, DOS, and so forth. The controls are not too di½cult to use, although it will probably be necessary to read the manual. The display can be saved as a postscript ®le. Viewkel is useful for generating illustrations for publication without color, but it does not have the quality of three-dimensional shaded rendering that is now common in commercial applications. Viewkel can also be used to display some results from the ADF program. At the time this book was written, Version 2.0 of viewkel was known to have some bugs, but Version 3.0 was not yet available.

The documentation is clearly written and generally adequate, although some of the less frequently used functions and utilities were not documented. The user should have a basic understanding of band structure theory before attempting to read the documentation.

Price category: free

Platforms: PC (Linux), Macintosh, RS/6000, HP-UX, SGI

Contact information: http://overlap.chem.cornell.edu:8080/yaehmop.html and [e-mail]

A.4 MOLECULAR MECHANICS/MOLECULAR DYNAMICS/MONTE CARLO SOFTWARE

The following are programs created speci®cally for force ®eld based simulations. There are also molecular mechanics programs bundled with the Spartan, Gaussian, and Hyperchem products discussed previously in this appendix.

A.4.1 MacroModel

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command ®le. The command ®le structure allows very complex simulations to be performed. The XCluster utility permits the analysis and ®ltering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough.

The force ®elds available are MM2*, MM3*, AMBER*, OPLSA*, AMBER94, and MMFF. The asterisk (*) indicates force ®elds that use a modi®cation of the original description in the literature. There is support for user-de®ned metal atoms, but not many metals are prede®ned. MM2* has atom types for describing transition structures. The user can designate a substructure for energy computation.

A.4 MOLECULAR MECHANICS 345

MacroModel can be used to run molecular mechanics minimizations, Monte Carlo simulations, and molecular dynamics simulations. The GB/SA solvation model is available. Several conformation-searching options are also available, including the low-mode conformation-search algorithm that is useful for ring systems. A free energy perturbation method exits for computing the DG between two systems when there is only a small di¨erence between them. The user must manually construct an ASCII command ®le in order to run free energy calculations. Alternatively, the MINTA algorithm can be used for the direct calculation of conformational and binding free energies. MINTA is not limited by the constraints of perturbation theory. Some tasks can be distributed over a cluster of workstations.

Our reviewer felt the molecule builder was easy to use. It is set up for organic molecules. Specialized building modes are available for peptides, nucleotides, and carbohydrates. It is also possible to impose constraints on the molecular geometry. Functions are accessed via a separate window with buttons labeled with abbreviated names. This layout is convenient to use, but not completely self-explanatory. The program is capable of good-quality rendering. At the time of this book's publication, a new three-dimensional graphic user interface called Maestro was under development.

Price category: production and higher Platforms: SGI, RS/6000

Contact information: SchroÈdinger, Inc. 17 She½eld Drive

West Grove, PA 19390 [phone] http://www.schrodinger.com/ [e-mail]

A.4.2 MOE

MOE (Version 2000.02) stands for molecular operating environment. The developers of this package took the unique approach of creating a programming language for writing molecular modeling software. The package currently includes molecular mechanics, dynamics, periodic boundary conditions, QSAR, a combinatorial builder, and many functions ideal for protein modeling, including multiple-sequence alignment and homology model building. Functions are also available for computing polymer properties and di¨raction patterns. Several conformation search routines are included. Other property calculations include log P and molar refractivity calculation.

The graphic interface is a multitasking environment that works well. The protein and carbohydrate builders are particularly convenient to use. The small-molecule builder has a selection of common organic functional groups as well as individual atoms for organics and common heteroatoms. There are a

346 APPENDIX A SOFTWARE PACKAGES

number of rendering modes to create fairly nice graphic images. However, the program does not have a way to save the display as an image ®le. MOE can be accessed through a Web browser also.

The force ®elds available are AMBER '89, AMBER '94, MMFF94, and PEF95SAC. The user can control scale factors, cuto¨ distances, and which terms are included in the force ®eld. It can also include customized parameters. The program would automatically generate force ®eld parameters if literature values were not available. This is convenient, but the user must be cautions about employing these parameters. No warning messages are generated when this happens, so the user must check the missing parameter report screen.

The QSAR utilities include functions for molecular diversity, similarity, and clustering. Both twoand three-dimensional pharmacophore ®ngerprinting techniques are available. It also includes the binary QSAR method designed for high-throughput screening. The ``hole ®ller'' function generates a new database that spans the diversity of multiple existing databases. Correlation and contingency analysis are available to determine which descriptors should be used. Over 130 descriptors are available, which include geometry, surface areas, topological indices, energy contributions, log P, refractivity, and charge density description. The program was not able to compute descriptors requiring semiempirical or ab initio computations.

QSAR, high-throughput, and combinatorial studies are aided by the program's ability to work with a large database of molecules. Substructure searches and ¯exible alignment checks can be run on the database. Individual entries in the database can be very large, making it possible to store detailed ®ngerprinting data for large molecules.

The SVL programming language (scienti®c vector language) is a byte-code interpretive language that can be run interactively or from an ASCII ®le. The language syntax is a combination of C‡‡ and scripting language conventions. The language includes vector arithmetic, molecular structure data types, a small amount of symbolic manipulation, pattern matching, and graphic display commands. This interpretive mode works well for molecular mechanics, but it would probably be too sluggish for ab initio calculations unless a native compiler is included in future versions. The SVL command language and the capacity to run MOE in batch mode (without the graphic interface) provide for the ability to automate tasks. All the functions accessed from menus in the GUI are running SVL program ®les. This open architecture makes it easy for others to add their own functions or modify the existing routines. The platform independence; access via GUI, batch, and Web; and ¯exible customizable architecture make MOE ideal for corporate deployment accessible to all researchers.

The documentation is well done. It includes function references, tutorials, and a how to section.

Price category: contact

Platforms: PC (Windows and Linux), SGI, Sun, HP-UX