Table Of Contents

  1. 1. Running NAMD
  2. 2. Compiling NAMD

1.  Running NAMD

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is based on Charm++ parallel objects. For any further information see this page.

NAMD version 2.6 is available on our infrastructure as a ready-to-use module. This version of NAMD was compiled with the Intel Fortran Compiler 10.1 and full MPI support. A machine optimized single precision version of the FFTW version 2.1.5 library was used. You can load NAMD by simply typing

$ module load namd

and the module will provide the path to the executables. You don't need to load any other modules in order to use NAMD as the module will take care to configure the working environment properly. To run NAMD non-interactively you should just include in your PBS scripts a line like the following

mpirun -x PATH -x LD_LIBRARY_PATH namd2 < infile.dat > outfile.dat

and the program will run fine. I you want to check what MPI libraries are being used by NAMD use the module list command.

The same version of NAMD is available also with meta-dynamics support enabled. To load this alternative version you need to type

$ module load namd/2.6-meta

and use the same command as above in your PBS scripts.

2.  Compiling NAMD

  1. compilare charm++
  • modificare ./charm-5.9/src/arch/mpi-linux-amd64/conv-mach.sh
  • ./build charm++ mpi-linux-amd64 --no-build-shared -O0
  1. compilare namd
  • modificare Make.charm indicando .rootdir/charm5.9 come dir
  • modificare ./arch/Linux-amd64-MPI.arch con i compilatori/opzioni giuste
  • modificare ./arch/Linux-amd64.fftw con la locazione di fftw 2.1.5 float
  • ./config fftw Linux-amd64-MPI
  • cd Linux-amd64-MPI
  • make