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NAMD (Not (just) Another Molecular Dynamics program) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations.

Release:April 2012
Lizenz:University of Illinois license
Developer:Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)
Version Compiler MPI FFT Library Path
2.9 GCC 4.7.0 intelmpi /cluster/Apps/NAMD/gcc_4.7.0/impi_4.0.3.008/
OpenMPI 1.6.1 /cluster/Apps/NAMD/gcc_4.7.0/openmpi_1.6.1/
Intel Composer 2011 SP1 10.319 intelmpi FFTW_3.3.3 /cluster/Apps/NAMD/intel-studio-2011-sp1-10/impi_4.0.3.008/

To use NAMD you need to load the corresponding modulefiles and then

$ $PATH/namd2 <configfile>

For parallel usage with LSF

$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun.lsf $PATH/namd2 <configfile>
  • software/namd2.1360838635.txt.gz
  • Last modified: 2013/02/14 11:43
  • by ulges