NAMD 2.7 New Features


The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a scalable, object-oriented molecular dynamics code designed for high-performance simulations of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources.

NAMD 2.7 offers several novel features:

  • Collective variable-based calculations (Colvars)
Definition of an arbitrary number of collective variables for multidimensional analyses and biased simulations. Current collective variables available in Namd 2.7 include Euclidian distances, projected distances on an axis or in the plane perpendicular to the latter, three-dimensional distance vectors, angles, torsions, eigenvectors, gyration radii, coordination,  root mean-square displacements (RMSD), orientations and alpha-helicity. New variables can be introduced without the need of recompiling NAMD.

Free-energy surfaces or potentials of mean force (PMF) can be constructed using a variety of methods, which currently include meta-dynamics, the adaptive biasing force (ABF) method, umbrella sampling and steered molecular dynamics (SMD). The Colvars module allows multiple, concurrent tasks to be executed in a single run - e.g. free energy integrations,  histograms collection and correlation functions plotting at the same time - with the possibility of visualizing the results during runtime without any post-processing.

At variance with NAMD 2.6, ABF calculations are no longer handled by a suite of external Tcl routines, but are performed in the core of the program, thereby gaining significantly in efficiency and allowing more complex model reaction coordinates to be defined.
  • Free energy peturbation (FEP) and thermodynamic integration (TI) methods for alchemical transformations
Introduction of TI for alchemical transformations with the dual-topology paradigm. Inclusion for both FEP and TI formalisms of a soft-core correction to circumvent singularities in the van der Waals potential caused by growing particles ("end-point" catastrophes). This implementation also includes the definition of separate grids in the framework of the particle-mesh Ewald method to account for this correction in long-range electrostatics. Addition of this feature to NAMD 2.7 results in increased accuracy and efficiency of the free-energy calculations.
  • GridForces methodology and molecular dynamics flexible fitting (MDFF)
Definition of external potentials discretized on multiple, finite grids. The user can arbitrarily select a subset of atoms onto which these potentials act, which, for instance, can be utilized in the context of mean-field descriptions of the environment.

Among the variety of applications for the GridForces methodology is MDFF, which allows the user to fit high-resolution structures into volumetric, low-resolution density maps to reconcile crystallographic and electron microscopy data.
  • Introduction of  additional bonded terms (ExtraBonds)
Arbitrary definition of bonded terms, i.e. chemical bonds, valence angles or torsional angles, without the explicit requirement to modify the topology at the level of the PSF structure file. This feature offers the possibility, among others, of creating artificial bonds between chemical groups that are not normally connected.
  •  Streaming SIMD extensions (SSE) constraint solver
Acceleration of the Shake and Settle (water) holonomic constraint algorithms using SSE instructions on compatible processors.
  • Enhanced performance and scalability
Implementation of novel load balancers, which results in improved scaling on small systems, i.e less than 50,000 atoms. Modifications of the patch distribution scheme to enhance the performance of sparse simulations, e.g. coarse-grain simulations.
  • CHARMM Drude polarizabile force field
  • TIP4P water model

NAMD 2.7 is available from http://www.ks.uiuc.edu/Research/namd/.

For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. 

Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu.

We look very much forward to hearing from you. Thank you for using our software!