Q-Chem: A Quantum Leap into the Future of Chemistry
  1. A hybrid Quantum Mechanical / Molecular Mechanical (QM/MM)[1],[2],[3] potential energy function with ab initio (HF, MP2, CCSD) and Density Functional Theory (DFT) capacity has been implemented in the CHARMM[4] and Q-Chem[5] software packages. We have also modified CHARMM and Q-Chem to take advantage of the newly introduced Replica/Path (RPM)[6] and the Nudged Elastic Band (NEB)[7] methods. These powerful techniques allow reaction pathways to be studied in a highly parallel (i.e. parallel/parallel) fashion where each pathway point can be distributed on a different processor(s) of a beowulf cluster.
  2. Type(s) of applications that it is good for. Some features are more for a specific type of problems.
    The usefulness of QM/MM methods is widely documented. To give a few examples:
    1. Examination of protein active sites that cannot be accurately studied via classical or semi-empirical QM/MM methods.
    2. Examination of solvation effects by running molecular dynamics on a molecule of interest surrounded by static or polarizable water models.
    3. Examination of reaction pathways via QM/MM scheme. This can be interesting for looking at bond-making/bond-breaking in protein active sites and/or for examining solvated reaction paths of things normally only studied in the gas phase.
    Another nice feature is that the development of Q-Chem and CHARMM is encapsulated so that any new feature implemented in CHARMM and/or Q-Chem can be used within QM/MM as well. This only occurs because the interface between the programs is rather general and flexible.
  3. Ability to run parallel/parallel reaction path calculations. For example, a reaction path can be divided up into X number of points. The X number of points can be run with the QM/MM Replica Path and Nudged Elastic Band methods where each point can be run on N number of processors (where n=any integer) in parallel. This is massively parallel and can efficiently take advantage of hundreds of processors.
  4. CHARMM has 3 ab inito packages interfaced to perform QM/MM calculations: Q-Chem, Gamess-US, and Gamess-UK.
  5. CHARMM has 3 ab inito packages interfaced to perform QM/MM Replica Path calculations: Q-Chem, Gamess-US, and Gamess-UK.
  6. CHARMM has 2 ab inito packages interfaced to perform QM/MM Nudged Elastic Band calculations: Q-Chem and Gamess-UK.
  7. 6. Application limit. Practical limit on size.
  8. The use of CHARMM and Q-Chem to perform QM/MM calculations is only limited by the number of point charges Q-Chem can handle.
  9. 7. Limit: derivatives, basis angular momentum, etc.
  10. The QM/MM functionality of Q-Chem needs derivatives to perform QM/MM minimizations and dynamics. Therefore, the limitations are due to the size of the QM system Q-Chem can handle (i.e. number of atoms and angular momentum).
  11. 8. Estimated application scope. Some features may not be used too often by most users. Others may have a wide usage.
  12. Predicted to be most used for:
    1. QM/MM minimizations
    2. QM/MM molecular dynamics
  13. Predicted to be less frequently used:
    1. QM/MM Replica Path
    2. QM/MM Nudged Elastic Band

Bibliography

  1. 1: Warshel, A. and Levitt, M., Theoretical Studies of Enzymic Reactions - Dielectric, Electrostatic and St, Journal of Molecular Biology, 103, 1976.
  2. 2: Singh, Rina and Just, George, The Synthesis of a 10-membered Benzo-oxadiyne Ring, Tetrahedron Lett., 31(2), 1990.
  3. 3: Field, M.J; Bash, P.A.; Karplus, M., , JOURNAL OF COMPUTATIONAL CHEMISTRY, 11, 1990.
  4. 4: Brooks, B. R. and Bruccoleri, R. E. and Olafson, B. D. and States, D. J. an, Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Ca, Journal of Computational Chemistry, 4, 1983.
  5. 5: J. Kong, C. A. White, A. I. Krylov, C. D. Sherrill, R. D. Adamson, T. R. Fu, Q-chem 2.0: A high-performance ab initio electronic structure program packa, Journal of Computational Chemistry, 21, 2000.
  6. 6: Woodcock, HL and Hodoscek, M and Sherwood, P and Lee, YS and Schaefer, HF a, Exploring the quantum mechanical/molecular mechanical replica path method:, THEORETICAL CHEMISTRY ACCOUNTS, 109, 2003.
  7. 7: Chu, JW and Trout, BL and Brooks, BR, A super-linear minimization scheme for the nudged elastic band method, JOURNAL OF CHEMICAL PHYSICS, 119, 2003.

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