1. The Scientific Computing Resource Center
  2. The NIH Network
  3. NIH Hardware Platforms
  4. Molecular Modeling Support Staff
  5. Training
  6. Documentation and Publications

The Scientific Computing Resource Center

The Scientific Computing Resource Center (SCRC) is a major gateway to molecular modeling resources at the NIH, including hardware, software, and documentation. The SCRC is located in Bldg. 12A/Room 1050 (402-3489). Entrance to the SCRC is strictly by appointment!

The NIH Network

 Selected software can be remotely accessed through the campus network. Certain products are maintained on the various central machines at NIH, and can be accessed from a personal computer using standard terminal emulation software, such as Versaterm Pro, or X-Window emulation software, such as Mac-X. In such cases, the computations are performed on the central computer.

Other software packages are maintained on "server" machines at DCRT, and require users to have a local Unix workstation of the appropriate type in order to be accessed via the network. In such cases, the computations are performed on the local workstation, with the server acting as a centralized storage place for the software. Server-based software can be simultaneously shared by a set number of users from any network access point at NIH. Sharing expensive software through the campus network can be highly cost effective, and will be increasingly pursued by DCRT. Currently, the QUANTA/CHARMm package is available in this manner, supporting up to 8 simultaneous users.

NIH Hardware Platforms

In addition to the numerous Unix workstations and personal computers distributed throughout the NIH ICDs, there are a number of centrally located computers and peripherals.

DCRT

Helix Systems (The High Performance Computing Section)

  1. Silicon Graphics Challenge XL:

    • Host name = "Helix".
    • Available over the NIH network.
    • Easy to obtain an account (4-DCRT for info).

  2. Convex C3830:

  3. Intel iPSC/860 parallel supercomputer:

Laboratory of Structural Biology, Molecular Graphics & Simulation Section

  1. Hewlett-Packard 750 parallel cluster:

National Cancer Institute Frederick Biomedical Supercomputing Center

  1. Cray Y-MP 8D/8128 supercomputer:

  2. Convex C3220:

  3. VAX Cluster:

NIH Molecular Modeling Support Staff

Full-time SCRC staff members are available in the facility Monday-Thursday, 8:30 AM to 4:30 PM. Technical assistance by SCRC staff is limited. More extensive technical assistance is available from DCRT scientists, primarily the Computational Molecular Biology Section (CMB), on a consulting basis.

The CMB offers consulting and support for scientists who require limited assistance with such tasks as defining a molecular modeling project, selecting and using software tools, and interpretation of results, but who are otherwise willing to perform their own work in the SCRC or elsewhere.

The CMB can perform in-depth molecular modeling work on a very limited number of projects. If you are unable to do your own molecular modeling work, the CMB will collaborate on a first-come-first-served basis. Waiting times for starting and completing such projects can be substantial.

The current support staff consists of:

DCRT's Computational Molecular Biology Section (CMB):

Other modeling assistance may be obtained through:

Training

In-house Training in Molecular Modeling

Five instructional seminars are offered periodically by the Computational Molecular Biology Section of DCRT. These are "Introduction to Molecular Modeling" (approx. 3 hours), "Introduction to QUANTA" (approx. 3 hours), "Introduction to SYBYL" (approx. 3 hours), "Introduction to Molecular Graphics" (approx. 3 hours), and "GCG Sequence Analysis on the Convex" (approx. 2.5 days). DCRT also sponsors a week-long intensive course entitled "Molecular Modeling Using QUANTA and CHARMm" (Dr. Don Kyle, Scios Nova, Inc.). Other relevant training seminars conducted by DCRT organizations are offered from time to time. A course catalogue is available from the DCRT Training Unit (4-DCRT). The current schedule of training sessions is advertised in the Yellow Sheet and the NIH Gopher server.

Outside Training in Molecular Modeling

If your training needs are more immediate, you can arrange to attend one of the off-site sessions organized by a software company. Such courses are held several times per year in various cities around the country, and typically cost around $1,000-$2,000 per person plus travel expenses.

The American Chemical Society periodically sponsors short courses in computational chemistry. One such course "Molecular Modeling: Methods and Techniques" is held on an annual basis at the University of Georgia, Athens, GA. The cost is approximately $2,000 plus expenses. Other American Chemical Society sponsored courses are presented via video teleconferences or during national meetings of the Society.

In-house Computer Training

Since most major molecular modeling software runs under the Unix operating system, it is important to have at least a rudimentary knowledge of Unix commands for logging in, dealing with disk files, etc. Computer training is available through the DCRT Training Unit. Courses of interest include "Fundamentals of Unix," "DCRT Support for Unix Workstations," "Introduction to the Convex Supercomputer," and "Introduction to Parallel Computing."

Documentation and Publications

Software Documentation

Software manuals for software supported by the SCRC are available for use in that facility. Personal copies of documentation for GAUSSIAN and GAMESS are available from the Technical Information Office located in Building 12A/1015; Ready-made photocopies of QUANTA/CHARMm manuals are available from the CMB or SCRC. SYBYL manuals are available from the CMB for duplication. In some cases, because of copyright restrictions, you will need to obtain documentation from the respective software suppliers.

Molecular modeling software product information is compiled on an ongoing basis by the CMB, and is maintained in a notebook in the SCRC.

Some molecular modeling software suppliers periodically distribute newsletters. The SCRC currently receives newsletters from Molecular Simulations, Inc. (QUANTA/CHARMm), Tripos (SYBYL), Biosym (Insight II/Discover), and Chemical Design Ltd. These publications, together with product literature, are kept on hand in the SCRC.

Home-Grown Instructional Materials (can be obtained from the CMB):

  1. "Introduction to Molecular Modeling" course notes, April, 1994.
  2. "Introduction to Molecular Graphics" course notes, August, 1994.
  3. "Introduction to QUANTA" course notes, March, 1994.
  4. "Introduction to SYBYL" course notes, August, 1993 (only available on-line in the SCRC).
  5. "Molecular Modeling Using QUANTA and CHARMm" course notes by Dr. Don Kyle, March 1993.
  6. "Introduction to GCG - Sequence Analysis on the NIH Convex System," Parts I and II, November, 1992.
  7. "NIH Gopher Seminar and Demo", October 1992.
  8. "CHARMM" course notes by Dr. Bernard Brooks et al, 1991.
  9. "Quantum Mechanics" course notes by Dr. Bernard Brooks et al, 1992.