Free md software for mac

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Mac OS X, UNIX, or Windows, is distributed free of charge, and includes source code.
VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.
VMD is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities.
VMD includes built-in support for high-end quad-buffered stereoscopic rendering which can be used in projection theatres as well as desktop graphics workstations.
Sterescopic display aids significantly in the perception of three dimensional structures and has been a key feature in VMD since its first release. VMD also provides support for inexpensive game-oriented stereo glasses, and even anaglyphic (Red/Blue) stereo.

Main features:
- No limit on the number of molecules, atoms, residues or number of animation frames, except available memory.
- Many molecular and volumetric rendering and coloring methods.
- Extensive atom selection language with boolean and algebraic operators, regular expressions, distance based selections, and more.
- Extensive graphical and text interfaces to Tcl, Tk, and Python to provide powerful scripting and analysis capabilities.
- High-quality on-screen rendering using OpenGL programmable shading on advanced graphics accelerators.
- Stereoscopic display with shutter glasses, autostereoscopic flat panels, anaglyph stereo glasses, and side-by-side stereo viewing.
- 3-D interactive control through the use of joysticks, Spaceballs, haptic devices and other advanced input devices, with support for Virtual Reality Peripheral Network (VRPN).
- An extensible plugin-based file loading system with support for popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR, and many others, as well as automatic conversion through Babel.
- Export displayed scene to extenal rendering formats including POV-Ray, Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well as STL or VRML2 files for 3-D printing.
- Integration of multiple sequence alignment and evolutionary analysis tools, in the form of the Multiseq plugin and its related toolset.
- Perform interactive molecular dynamics (IMD) simulations using NAMD, Protomol, or other programs as simulation back-ends.
- Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD. See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd
- Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that collaborators can work together over the internet. See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore.

Version restrictions:
- You have to register in order to download.

Enhancements
- User documentation updates
- Minor improvements and corrections to the VMD Users Guide, added documentation for new commands and environment variables.
- New and updated tutorials available for advanced images and movie making, 3-D PDF export, Tachyon ambient occlusion lighting, electrostatic surface coloring, and density map based atom selections.
- User interface changes
- New "User" picking mode for use with user defined scripts and plugins
- General Improvements
- Support for 3-D capture with Acrobat 3-D, for creation of documents which embed 3-D molecular structures.
- VMD renderings can now use Tachyons advanced ambient occlusion lighting for tremendously improved 3-D renderings of molecular graphics. This advanced lighting mode can greatly enhance the shading of pores and channels, structures with cavities, and other cases which typically require the use of depth cueing for better depth perception.
- VMD now supports the nVidia "Gelato" GPU-accelerated production quality rendering package. VMD exports scenes in Gelatos native PYG file format, as well as the RenderMan RIB format.
- By default VMD will now use all of the available processors to accelerate parallelized portions of the code which currently include several structure analysis routines, Interactive MD, and ray tracing.
- Overall per-atom memory use has been significantly decreased. VMD now uses just over half as much memory per atom compared with previous versions, leaving more space available for additional trajectory frames or for more molecules to be loaded at once.
- VMD structure loading and analysis scalability have been significantly improved. VMD has been successfully tested loading and analyzing structures of up to 72,000,000 atoms.
- Automatic bond determination algorithm now runs up to 3 times faster on single processor systems, and uses multiple processors for improved performance on multicore processors and multiprocessor workstations.
- Drastically improved multi-thousand-file structure loading performance when display update is disabled. This benefits batch mode VMD analysis jobs involving analysis of thousands of structures, e.g. loading and searching large subsets of the PDB.

Imagine being able to harness the power of Machinedrums synthesis engine with your Mac. This dream is now a reality! MD Machine Lab allows you to create, tweak, and save individual machines (drum sounds) on your Mac!
MD Machine Lab provides a slick, easy-to-use interface, giving you complete control over your sonic design.
Main features:
- Randomize
- The randomize feature of MD Machine Lab gives you the ability to set machine parameters to random values. Additionally, you get to choose which parameters get randomized!
- Internationalized
- Speak a language other than English? No problem! MD Machine Lab supports many different languages, including French and German.
- Fast and Lightweight
- I developed MD Machine Lab on a 400 MHz iMac DV SE. While its not THE slowest machine out there, its still pretty freakin slow! Therefore, ensuring that my programs run as efficiently as possible is a top priority. MD Machine Lab is a Cocoa application, written entirely in Objective-C. Furthermore, its multi-threaded, and includes optimizations for both the G4 and the G5.
- Undo! Undo!
- Make a mistake? No worries: MD Machine Lab features unlimited levels of undo and redo! This means you can tweak all you want, without fear of losing a precious creation.
- Randomize!
- The randomize feature of MD Machine Lab gives you the ability to set machine parameters to random values. Additionally, you get to choose which parameters get randomized!
- Internationalized
- Speak a language other than English? No problem! MD Machine Lab supports many different languages, including French and German.
Enhancements:
- fixed a major bug in "Import From SysEx File..." where parameter values werent being set correctly for any machines with less the 8 synthesis parameters. Thanks goes to Jin Lee for the bug report :)
- hitting command-alt-w now closes all windows.

Requirements:
System 7.1 or later, Alps MD-4000 Scanner.

Requirements: Mac OS X 10.4.11 or later.

jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs.
jSim has a project style interface to organize your md simulations. jSim is also possible to start md simulations on remote computers with ssh.

Enhancements
- fixed tooltip bug in grmsf
- fixed trjcat command bulding bug
- fixed ssh file chooser bug
- fixed import ssh bug Fixed in Version 0

Xfile Test Drive 2.0.1.10 provides you with a useful file manager for Mac OS X capable of seamlessly handling all file systems and the only file manager for Mac OS X capable of detailing and allowing access to all file system information. It's the only file manager capable of detailing all file information available on OS X - and offering full editing capabilities for all these system features.

Major Features:

1. Runs so smooth on Leopard. Like no other file manager.
2. Manages 'file flags' (user and system append, immutable, etc); 'sticky bits'; set user and group ID bits; it displays major and minor device numbers, inodes (CNIDs), number of links, blocks used, optimal block sizes, and file generation numbers for the superuser; it creates both hard and symbolic links.
3. All of this is supported by your operating system. Almost none of it is supported by any other file browser. Especially Apple's Finder.
4. Additional utilities included allow manipulation of two Unix and five HFS time stamps; batch and recursive mode and time stamping; the remarkable Xshelf; the comprehensive 'post mortem' analysis tool Tracker; complete access to 'legacy MacOS' filesystem data; and more.
5. Also includes the file system scanner Xscan for quickly locating items in the file systems and for conducting perfunctory system security audits. Xscan can scan an entire OS X computer, listing all files in eleven columns of file data, in a time span of one or two minutes even on 'yesterday's hardware'. It can also scan entire networks at the same speed.
6. All items with resource forks are clearly marked with sizes for each fork available. The FileInfo utility allows manipulation of the special 'Finder flags' found in HFS catalog node info blocks.
7. Xstrings dumps readable strings from binary files; Xfind searches given files for specified search strings. And so forth.
8. All the utilities are tightly integrated - so if you can conceive of a way they work together, they probably do.
9. Comes with the proprietary ACP framework, offering seamless search capabilities in every program, full management of both the imagery and documentation systems, and more. Information on the full ACP is also available.
10. Be part of the ACP - Rixstep's 'Apple Core Project', a research project into viable means to hone and optimise generic application development on OS X for professional purposes. The ACP is intended for the professional audience but extreme power users can also find benefit.
11. Be part and parcel of the complete ACP and offers insight into the full capabilities of this award winning product. The Xfile application is the fastest file manager for OS X, capable of listing a full ten columns of file system data for 10,000 files in one second real time. It's known as the 'standard setter' for OS X file management. As it's the only file manager capable of doing everything possible on OS X, it stands in a class of its own.
12. Package Contents: Contains 290+ items. In addition to Xfile and the ACP framework it contains the applications FileInfo, MD, Rixcomp, Rixmode, Rixstamp, TMI, Tracker, Xattrib, Xfind, Xscan, Xsed, Xshelf, Xstamp, Xstrings, and Undercover.

Requirements

• OS X universal 10.4.0 or later (Tiger, Leopard, Snow Leopard);
• Very little disk footprint; extremely frugal on RAM.