NAMD
NAMD is a open source parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, GROMACS and X-PLOR.
• Efficient conjugate gradient minimization.
• Fixed atoms and harmonic restraints.
• Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.
• Constant temperature via rescaling, coupling, or Langevin dynamics.
• Constant pressure via Berendsen or Langevin Nose-Hoover methods.
• Particle mesh Ewald full electrostatics for periodic systems.
• Symplectic multiple timestep integration.
• Rigid waters and bonds to hydrogen atoms.
• Chemical and conformational free energy calculations.
• Locally enhanced sampling via multiple images.
• Interactive visual steering interface to VMD.
Tutorial files are available at /app1/ia32-64/vmd-1.8.5/proteins. For convenience, you can make a copy in your home directory:
mkdir proteins
cp -r /app1/ia32-64/vmd-1.8.5/proteins proteins
Follow the tutorial and sample files to construct the input file myjob.conf.
To submit a batch job
bsub -q linux64 –o myjob.o “namd2 myjob.conf > myjob.out”
You may need some standard parameter or topology files which you can copy into your directory from:
/app1/ia32-64/NAMD_2.6_Linux-amd64/toppar
Please feedback problems to ccehpc@nus.edu.sg.