software:namd2

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software:namd2 [2013/02/14 10:59]
ulges
software:namd2 [2021/09/14 15:07]
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 ====== NAMD ====== ====== NAMD ======
-[[http://www.ks.uiuc.edu/Research/namd/]]\\ \\+[[http://www.ks.uiuc.edu/Research/namd/]]\\
  
-NAMD (Not (just) Another Molecular Dynamics program) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. +NAMD (**N**ot (just) **A**nother **M**olecular **D**ynamics 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.+Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations.\\
  
 +^  NAMD  ^^
 +|**Version:**|2.9|
 +|**Release:**|April 2012|
 +|**Lizenz:**|[[http://en.wikipedia.org/wiki/University_of_Illinois_license|University of Illinois license]]|
 +|**Developer**:|Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)|
  
 +
 +===== Available Versions and Combinations =====
 +
 +^ Version ^ Compiler                   ^ MPI                                            ^ Path                                        ^ Environment^
 +| 2.9   | [[software:gcc|GCC]] 4.7.0 | [[software:intelmpi|intelmpi]] 4.0.3.008 |''/cluster/Apps/NAMD/gcc_4.7.0/impi_4.0.3.008/'' | |
 +| :::   | :::                        | [[software:openmpi|OpenMPI]] 1.6.1       |''/cluster/Apps/NAMD/gcc_4.7.0/openmpi_1.6.1/''  | |
 +| :::   | :::                        |                                          |''/cluster/Apps/NAMD/gcc_4.7.0/ibverbs/''  | |
 +| :::   | [[software:icc|Intel Composer]] 2011 SP1 10.319 | [[software:intelmpi|intelmpi]] 4.0.3.008 |''/cluster/Apps/NAMD/intel-studio-2011-sp1-10/impi_4.0.3.008/''| I_MPI_FABRICS=shm:ofa((This version of NAMD will be faster, if you set the Intel-MPI runtime environment variable I_MPI_FABRICS to shm:ofa. Just type ''export I_MPI_FABRICS=shm:ofa'' in your console and then run Namd)) |
 +===== Usage =====
 +To use NAMD, you first need to load the corresponding modulefiles.\\
 +
 +For single-cpu usage: 
 +<code bash>$ $PATH/namd2 <configfile></code>
 +
 +For parallel usage with LSF:
 +<code bash>$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun $PATH/namd2 <configfile></code>
 +
 +===== Notes =====
 +For computations with up to around 256 cores the version ''gcc_4.7.0/impi_4.0.3.008/'' will be faster than ''intel-studio-2011-sp1-10/impi_4.0.3.008/''.
 +With a higher number of cores it will be reversed.