The Role of a Molecular Modeling Specialist Molecular Modeling is an experimental technique, similar to "wet lab" techniques. Unlike other experiments, molecular modeling will always generate a result. In fact, the generation of a result has become very easy with modern molecular modeling software. Yet theories and strategies have also become more complex, requiring the expertise of a molecular modeling specialist to judge the result: Have proper techniques been used (is the result accurate?) Have proper controls and control experiments been used (is the result reliable or significant?) Are there limitations: If not all possibilities are calculated, has the modeler searched enough of parameter space? If the results depend on a basis set, has the modeler limited the modeling to a parameter space that is too small? Therefore, the result depends as much on the quality of the modeler as the quality of the technique. This course is designed as an introduction to more specialized molecular modeling techniques for those who want to investigate particular molecular modeling methods in greater detail.

Computing

• development of computational theory of physical states
• development of molecular structure databases
• development of the computer

The computer conisists of:

1. Central Processing Unit {CPU}

   R4400, 180 MHz R5000, or 250 MHz R10000 CPUs

2. Memory

   64 to 256 MBytes

3. disk

   ~12 GBytes total and growing

4. Graphics processor

   XZ, Extreme, CRM, or MXEi graphics processors

5. monitor

   17 or 20 inch 1280x1024 resolution monitors

6. keyboard, mouse, other input devices
7. other drives

   CDROM, Zip, tape drives

8. network (10 Mbits/sec) or internal bus (40 MBytes/sec)

A networked computer can consist of one or more items from various sources. In practice, your workstation will consist of:

1. monitor, keyboard, mouse, CDROM drive of local workstation
2. CPU, memory, graphics processor of local workstation; on occasion, you will telnet to another workstation and use the CPU & memory of that workstation.
3. disk in remote workstation
   Your home directory on ALL workstations is named /ruser/instruct2/your_name and resides on pchem06.
   My home directory is named /ruser/nmr/mpagel and resides on nmr.
   The server directory is named /remote/server and resides on splatter and saturn.
   

1. UNIX workstations are easier to program and support

   Workstation	Relative Cost (time & resources)
   	Programming	Support
   UNIX	1	1
   WINTEL	3-5	2
   Mac	30-50	10

2. UNIX workstations have historically been used for scientific computing. Many molecular modeling applications run only on UNIX workstations.

3. WINTEL workstations now meet or exceed many of the specifications & benchmarks for particular parts of a desktop UNIX workstation. One exception is graphics performance---SGI workstations are still faster (although the gap between WINTEL and SGI workstations continues to decrease).

4. The INTERACTION of the parts of a workstation is still MUCH faster with UNIX workstations than with WINTEL workstations.

5. In my opinion, server-client computing will continue to be dominated by UNIX servers and WINTEL clients. The middle ground of high-end clients and low-end servers will continue to be a mixture of UNIX and WINTEL workstations.