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)
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
- GridForces methodology and molecular dynamics flexible fitting (MDFF)
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)
- Streaming SIMD extensions (SSE) constraint solver
- Enhanced performance and scalability
- 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 firstname.lastname@example.org.