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Practical Computer Help Topics

File Transfer and UNIX

Downloading Secture Shell Software

Running batch jobs

Using UNIX

Using vi editor

Using sftp (secure file transfer protocol)

Using ssh (secure shell remote login)

Download a job file

Using VMD and NAMD

Downloading and Running VMD

Understanding the PSF file

Understanding Topology and Parameter files

Using Menus in VMD

Setting up MD simulations using VMD

Setting up FEP calculations using VMD

Making a mutation using VMD

Using a Patch to setup NAMD input files

Using Tcl Commands in VMD

Using psfgen to generate NAMD input file with a single segment

Using psfgen to generate NAMD input file with different segments

Using Solvate to add water in PBC

Setup Periodic Boundary Conditions in a NAMD input file

Fortran code by Allen and Tildesley

Structures for analysis

Nucleic Acid Database

Protein Data Bank

Math Review

Using MAPLE

Differentiation: single and multivariable

Gaussian integrals

Moments of Gaussian integrals

Exponential integrals

Integration by parts

Stirling's approximation

The binomial distribution

Thermodynamics review

Web site, problems and exams from Thermodynamics Fall 1997

Web site, problems and exams from Thermodynamics Fall 1998

Last modified December 7, 2000