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MDTools is a collection of programs, scripts, and utilities
we provide for researchers to make various modeling and simulation
tasks easier, and to provide basic code and utilities which can be
built up into larger toolsets. Each tool, script, or library is
listed below and has its own separate distribution, documentation,
etc. The programs in this collection are provided for the benefit of
the research community, but are not officially supported unless
otherwise stated. Each program may have a software license and/or
citation suggestions which should be listed on its web page.
Simulation and Analysis Tools
| CatDCD |
Concatenates DCD multiple trajectory files, can select subset of atoms, think of Unix "cat". |
| Chemical2vmd |
Lets VMD act as a helper application for chemical/x-vmd MIME type in web browsers |
| Conect2psf |
Converts PDB "CONECT" records into a "PSF" file for proper bond display in VMD
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| FlipDCD/FixDCD |
DCD trajectory file endianism and header conversion |
| MDAPI |
Application programming interface for molecular dynamics simulation engines |
| MDTools for Python |
Protein structure and dynamics analysis classes |
| MatDCD |
A Matlab package for reading and writing DCD format trajectory files |
| Mindy |
A "minimal" molecular dynamics program based on the NAMD source code |
| Mol_Volume |
A program for calculating macromolecular volume |
| PDBCat |
A tool for PDB file text processing and conversion |
| SODIUM |
Arrange ions around biological macromolecules |
| Trio |
A molecular dynamics trajectory file converter |
| Wat2ions |
Places ions in a water bath. A companion program to Delphi. |
Web, Programming, and Administrative Tools
| DBI::Frame |
An extension of Perl DBI which a framework with better logging, and standardized interfaces to common operations |
| TB::AddressBook |
An address book database, written in perl, based on DBI::Frame |
| make_tn |
make_tn is a script used to create thumbnail images and a web page to
index them |
| Projector |
RS-232 control/automation software for Electrohome Marquee series CRT projectors |
| SoftDB |
A web-based, medium scale, field-specific software database |
| Sysload |
Machine load monitoring system for clusters, departments |
| Usagemon |
Software usage/event tracking system |
| Swing Test |
Java Swing Detection Applet for Web Browsers |
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