Tinker with Molecular Dynamics for Fun and Profit
All of these executables are designed to run as command-line programs. The output tends to be files of numbers, which are hard for a human to evaluate. The group who created TINKER also created a program called Force Field Explorer (FFE).
Figure 1. On initial startup, you will get an empty project window and a TINKER console.
The executables built above are not compiled to interface with FFE as is. If you want to compile your own copy and have it interact with FFE, it requires changing a number of source files. In this case, I would suggest that you go ahead and download one of the installation packages that include FFE. These come as a gzipped shell archive. After gunzipping it, you can run the shell script to start up the Java-based installer. It will let you select which portions to install along with FFE. Once it is all done, go ahead and start up FFE. It will open up the main window and a console window. From within FFE, you can load up structure files and start various TINKER analyses.
When you first open an .xyz file, the structure is rendered and displayed in the main window. You then can select the Modeling Commands tab to select which specific TINKER analysis to run. By default, these TINKER runs happen locally on the same machine, but it doesn't have to be this way. FFE gives you the option of connecting to a remote machine, likely more powerful than your desktop, and getting the actual TINKER programs to run over there.
Figure 2. You have access to all of the TINKER analysis routines, directly from FFE.
Once you have results, you can change the visual details like colors and whether to use wireframe or tube and so on. You also have the option of exporting a visual as an image file in one of several file formats.
I easily could fill the entire contents of Linux Journal just covering the most basic functionality TINKER provides. Hopefully, you will have seen enough to get an idea of whether this software might be of use to you. If so, a rather large amount of detailed documentation is available at the main TINKER Web site.
Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.
Fast/Flexible Linux OS Recovery
On Demand Now
In this live one-hour webinar, learn how to enhance your existing backup strategies for complete disaster recovery preparedness using Storix System Backup Administrator (SBAdmin), a highly flexible full-system recovery solution for UNIX and Linux systems.
Join Linux Journal's Shawn Powers and David Huffman, President/CEO, Storix, Inc.
Free to Linux Journal readers.Register Now!
- Download "Linux Management with Red Hat Satellite: Measuring Business Impact and ROI"
- Petros Koutoupis' RapidDisk
- ServersCheck's Thermal Imaging Camera Sensor
- The Italian Army Switches to LibreOffice
- Linux Mint 18
- Oracle vs. Google: Round 2
- The FBI and the Mozilla Foundation Lock Horns over Known Security Hole
- Privacy and the New Math
- Varnish Software's Varnish Massive Storage Engine
Until recently, IBM’s Power Platform was looked upon as being the system that hosted IBM’s flavor of UNIX and proprietary operating system called IBM i. These servers often are found in medium-size businesses running ERP, CRM and financials for on-premise customers. By enabling the Power platform to run the Linux OS, IBM now has positioned Power to be the platform of choice for those already running Linux that are facing scalability issues, especially customers looking at analytics, big data or cloud computing.
￼Running Linux on IBM’s Power hardware offers some obvious benefits, including improved processing speed and memory bandwidth, inherent security, and simpler deployment and management. But if you look beyond the impressive architecture, you’ll also find an open ecosystem that has given rise to a strong, innovative community, as well as an inventory of system and network management applications that really help leverage the benefits offered by running Linux on Power.Get the Guide