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OS: Linux, ...

License: Freeware

The MDTools suite is a collection of programs, scripts, and utilities to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets

Simulation 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
FlipDCD/FixDCD - DCD trajectory file endianism and header conversion
Ionize - Parallelized ion placement tool
JMV: Java Molecular Viewer - JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.
MDAPI - Application programming interface for molecular dynamics simulation engines
MDEnergy - Calculate energies from DCD or PDB files
MDTools for Python - Protein structure and dynamics analysis classes
MDX - Collection of C libraries to enable development of methods for molecular dynamics of biomolecules
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
volutil - manipuate 3D volumetric data in VMD
Wat2ions - Places ions in a water bath. A companion program to Delphi.