NAMD

Author

M. Bhandarkar, R. Brunner, C. Chipot, A. Dalke, S. Dixit, P. Grayson, J. Gullingsrud, A. Gursoy, D. Hardy, J. Hénin, W. Humphrey, D. Hurwitz, N. Krawetz, S. Kumar, M. Nelson, J. Phillips, A. Shinozaki, G. Zheng and F. Zhu

Origin

Theoretical Biophysics Group, University of Illinois and Beckman Institute, USA.

Version

NAMD Version 2.7 and 2.6

Official Web Site

http://www.ks.uiuc.edu/Research/namd/

Brief Program Description

NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology.

The following list gives a brief description of the features for this version of NAMD. For more information, users are referred to the User Manual.

• Force Field Compatibility

The force field used by NAMD is the same as that used by the programs CHARMM and X-PLOR. This force field includes local interaction terms consisting of bonded interactions between 2, 3, and 4 atoms and pairwise interactions including electrostatic and van der Waals forces. This commonality allows simulations to migrate between these three programs.

• Efficient Full Electrostatics Algorithms

NAMD incorporates the Particle Mesh Ewald (PME) algorithm, which takes the full electrostatic interactions into account. This algorithm reduces the computational complexity of electrostatic force evaluation from O(N²) to O(N log N).

• Multiple Time Stepping

The velocity Verlet integration method is used to advance the positions and velocities of the atoms in time. To further reduce the cost of the evaluation of long-range electrostatic forces, a multiple time step scheme is employed. The local interactions (bonded, van der Waals and electrostatic interactions within a specified distance) are calculated at each time step. The longer range interactions (electrostatic interactions beyond the specified distance) are only computed less often. This amortizes the cost of computing the electrostatic forces over several timesteps. A smooth splitting function is used to separate a quickly varying short-range portion of the electrostatic interaction from a more slowly varying long-range component. It is also possible to employ an intermediate timestep for the short-range non-bonded interactions, performing only bonded interactions every timestep.

• Input and Output Compatibility

The input and output file formats used by NAMD are identical to those used by CHARMM and X-PLOR. Input formats include coordinate files in PDB format, structure files in X-PLOR PSF format, and energy parameter files in either CHARMM or X-PLOR formats. Output formats include PDB coordinate files and binary DCD trajectory files. These similarities assure that the molecular dynamics trajectories from NAMD can be read by CHARMM or X-PLOR and that the user can exploit the many analysis algorithms of the latter packages.

• Dynamics Simulation Options

MD simulations may be carried out using several options, including:

Constant energy dynamics

Constant temperature dynamics via:

- Velocity rescaling

- Velocity reassignment

- Langevin dynamics

Periodic boundary conditions

Constant pressure dynamics via:

- Berendsen pressure coupling

- Nosé-Hoover Langevin piston

Energy minimization

Fixed atoms

Rigid waters

Rigid bonds to hydrogen

Harmonic restraints

Spherical or cylindrical boundary restraints

• Easy to Modify and Extend

Another primary design objective for NAMD is extensibility and maintainability. In order to achieve this, it is designed in an object-oriented style with C++. Since molecular dynamics is a new field, new algorithms and techniques are continually being developed. NAMD's modular design allows one to integrate and test new algorithms easily.

• Interactive MD simulations

A system undergoing simulation in NAMD may be viewed and altered with VMD; for instance, forces can be applied to a set of atoms to alter or rearrange part of the molecular structure.

• Load Balancing

An important factor in parallel applications is the equal distribution of computational load among the processors. In parallel molecular simulation, a spatial decomposition that evenly distributes the computational load causes the region of space mapped to each processor to become very irregular, hard to compute and difficult to generalize to the evaluation of many different types of forces. NAMD addresses this problem by using a simple uniform spatial decomposition where the entire model is split into uniform cubes of space called patches. An initial load balancer assigns patches and the calculation of interactions among the atoms within them to processors such that the computational load is balanced as much as possible. During the simulation, an incremental load balancer monitors the load and performs necessary adjustments.

Areas of Application

The main advantage of the package is that it is a molecular dynamics code enabling interactive simulation by linking to the visualization code VMD, and its capability of parallel scaling.

For recent changes to the package, please visit the NAMD website.

Implementation and Access

The command runnamd27 accesses and executes the computational chemistry program NAMD Version 2.7 (2010-10-15). NAMD runs both in serial and in parallel on Magellan.

Access is via the command runnamd27 as shown:

$CHEM/runnamd27 progname inputfile

where progname stands for namd2, the main simulation program or psfgen, the program for generating the PSF file and PDB file for use with namd2.

The previous version of NAMD Version 2.6 is still accessible via the command runnamd as shown:

$CHEM/runnamd progname inputfile

Machines

Available on Magellan.

Documentation

Documentation for NAMD is available from the directory $CHEM/doc/namd in PDF format, and can be downloaded directly from the NAMD web site. NAMD examples are located in the directory $CHEM/doc/namd/examples. Tutorials and example files can be found on the NAMD web site.

There are Unix-style man pages containing information on the local implementation of NAMD, accessible by typing: man runnamd27 for version 2.7 and man runnamd for version 2.6.

Literature References

References are listed in the NAMD User Manual.

Specialist Support

Dr Helen Tsui. Address: Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ. Tel: 020 7594 1220 Email: helen.tsui@imperial.ac.uk.

Program Restrictions and Comments

Users are required to include the following citation for NAMD in any reports or published results obtained with the software:

"NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

Any published work which utilises NAMD shall include the following reference:

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005.