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NAMD

Description

NAMD is a fast, parallel, and scalable molecular dynamics program designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge with source code. It is developed in conjunction with VMD. It is also file-compatible with AMBER, CHARMM, and X-PLOR.
Homepage: NAMD

Access

Loading the Module

There are a variety of NAMD modules supported on Grace/FASTER. For more information, see our modules page.

Make sure you have a clean environment before getting started:

[ NetID@cluster ~]$ml purge

To find what NAMD versions are available, use module spider:

module spider NAMD

To learn how to load a specific module version, use module spider: 

module spider NAMD/3.0

To load NAMD:

module load NAMD/3.0

To find what NAMD versions are available, use module spider:

module spider NAMD

To learn how to load a specific module version, use module spider: 

module spider NAMD/2.14

You will need to load all module(s) on any one of the lines below before the "NAMD/2.14" module is available to load.

GCC/8.3.0 CUDA/10.1.243 OpenMPI/3.1.4

Read more about toolchains.

Finally, to load NAMD:

module load GCC/8.3.0 CUDA/10.1.243 OpenMPI/3.1.4 NAMD/2.14

To find what NAMD versions are available, use module spider:

module spider NAMD

To learn how to load a specific module version, use module spider: 

module spider NAMD/2.14-mpi

You will need to load all module(s) on any one of the lines below before the "NAMD/2.14-mpi" module is available to load.

GCC/11.3.0 OpenMPI/4.1.4

Read more about toolchains.

Finally, to load NAMD:

module load GCC/11.3.0 OpenMPI/4.1.4 NAMD/2.14-mpi

To find what NAMD versions are available, use module spider:

module spider NAMD

To learn how to load a specific module version, use module spider: 

module spider NAMD/2.14-mpi

You will need to load all module(s) on any one of the lines below before the "NAMD/2.14-mpi" module is available to load.

GCC/12.3.0 OpenMPI/4.1.5

Read more about toolchains.

Finally, to load NAMD:

module load GCC/12.3.0 OpenMPI/4.1.5 NAMD/2.14-mpi

NOTE: Pay close attention to the information following the version number of the module. This is called the toolchain. This information describes what other modules will be loaded with NAMD. These modules will be disrupted by use of extraneous modules of different toolchains, so please purge all unnecessary modules prior to using NAMD.