Bio-molecular Dynamics (Molecular Modeling System)
Useful Molecular Dynamics or Molecular Modeling Software
- UCSF Chimera
- NAMD (Nanoscale Molecular Dynamics)
- VMD (Molecular Visualization)
- Gaussian 16 (Gaussian accelerated molecular dynamics)
UCSF Chimera
UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
NAMD + VMD
Nanoscale Molecular Dynamics is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems.
NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.
Installation & Configuration of UCSF Chimera
- First download UCSF Chimera using the following link;
https://www.cgl.ucsf.edu/chimera/download.html
Note: This software is available for both Windows & Linux platforms.
Simply extract files by double click on *.bin file which is downloaded.
Next run chimera by clicking on it.
Loading Sample Data (Tutorials are available in official documentation)
Finally ! You can manipulate sample
Installation & Configuration of NAMD + VMD
First download NAMD + VMD using the following link;
https://www.ks.uiuc.edu/Development/Download/download.cgi
Extract NAMD .tar.gz file
Open up NAMD_2.14_Linux-x86–64-multicore folder and execute namd2 file.
Installation & Configuration of VMD
Extract downloaded tar.gz file
Open up Terminal , navigate to vmd-1.9.3 directory and run the following command
./configure
Next navigate to /src directory and run the following command
Finally ! you are ready to run VMD, just navigate to /usr/local/bin and run vmd by clicking on it.
Note: you can use PDB sample data file for analysis.
