Related Packages
- VMD is used to visualize molecular structures and trajectories.
- Tcl is used within NAMD and VMD to provide scripting capabilities.
- FFTW may be compiled into NAMD for better PME performance.
- X-PLOR and CHARMM are useful for setup and analysis.
- The CHARMM parameters are available for use with NAMD.
- The Cornell et al. (AMBER) parameters are available in CHARMM format for use with NAMD.
Useful Scripts
- namdplot works with XMGR to plot energies, etc.
- This front-end simplifies running NAMD and even works with our DQS setup.
- These MATLAB scripts read and write DCD trajectory files.
Example Simulations
- Interactive BPTI (882 atoms, small)
(README,
config,
directory,
56k .tar.gz,
54k .zip)
- ER-GRE benchmark (36573 atoms, spherical)
(config,
directory,
1.1M .tar.gz,
1.0M .zip)
- ApoA1 benchmark (92224 atoms, periodic)
(config,
directory,
2.8M .tar.gz,
2.7M .zip)
- decalanin (66 atoms, tiny)
(config,
directory,
.tar.gz,
.zip)
- Tcl forces (decalanin)
(config,
directory,
.tar.gz,
.zip)
- PSF generation for BPTI
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