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How to Run NAMD

Input

You can use any text editor to make the appropriate input files for NAMD.

How to Run NAMD in Batch

How to Run NAMD from the UCLA Grid Portal

See How to Run an Application from the UCLA Grid Portal

How to Run NAMD from the Cluster Login Node using the Queue Scripts

The easiest way to run NAMD in batch from the login node is to use the queue scripts. See Running a Batch Job for a discussion of the queue scripts and how they are used.

The following queue scripts are available for NAMD:

namd.q
Asks you whether you want to run in parallel or serial.
namd.q.parallel
Runs in parallel.
namd.q.serial
Runs in serial.

How to Run NAMD from the Cluster Login Node Using UGE Commands

See Running a Batch Job for guidelines to follow to create the required UGE command file. Alternatively, you could create an UGE command file with one of the queue scripts listed above. After saving the command file, you can modify it if necessary. See Commonly-Used UGE Commands for a list of the most commonly used UGE commands.

How to Run NAMD Interactively

How to Run NAMD Interactively from the UCLA Grid Portal

See How to Run an Application from the UCLA Grid Portal

How to Run NAMD Interactively from the Cluster Login Node

To run NAMD interactively first obtain one or more interactive nodes with qrsh. Once you obtain a compute node, at its shell prompt enter:

/u/local/apps/namd/current/namd2

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