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How to Run Amber

Input

You can use any text editor to make the appropriate input files for Amber. If you are running Amber in batch, your Amber control file must end with the extension .files

How to Run Amber Interactively

How to Run Amber Interactively from the UCLA Grid Portal

See How to Run an Application from the UCLA Grid Portal

How to Run Amber Interactively from the Cluster Login Node

First start an interactive session on a compute node with the qrsh. Then at the compute node shell prompt, enter:

module load amber

or, if you have reserved multiple nodes:

module load amber-mpi

At the compute node’s shell prompt, enter your Amber or Amber Tools command. A list of about 50 Amber programs maybe found in the Amber User’s Manual.

For example, to run the Amber program sander, enter:

sander -O -i mdin -c inpcrd -o out -p prmtop

where:

  • mdin is the file that contains the control data
  • inpcrd contains the initial coordinates
  • out is the name of the output file
  • prmtop contains the molecular topology force fields

How to Run Amber-CUDA

First start an interactive session on a gpu node with qrsh. Then at the gpu node’s shell prompt, enter:

module load amber-cuda

At the gpu node’s shell prompt, enter your Amber or Amber Tools command.

How to Run Amber in Batch

To run Amber in batch, you are required to have a control file that names your input and output files. The control file must be named:

name.files

where name is any name you choose.

The content of the control file should be:

PROGRAM = amber_program
MDIN = min.in
INPCRD = omp.crd
MDOUT = min.out
PRMTOP = omp.top

where amber_program is an Amber program name, such as sander and the other names in italics are replaced by the names of your actual files.

How to Run Amber in Batch from the UCLA Grid Portal

See How to Run an Application from the UCLA Grid Portal

How to Run Amber in Batch from the Cluster Login Nodes using the Queue Scripts

The easiest way to run Amber in batch from the login nodes 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 Amber:

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

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

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. See Running a Batch Job for guidelines to follow to create the required UGE command file.

February 2011

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