- How to Run Amber Interactively
- How to Run Amber-CUDA
- How to Run Amber in Batch
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 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
- 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
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.
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:
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
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
How to Run Amber in Batch from the Cluster Login Nodes using the Queue Scripts
The following queue scripts are available for Amber:
- Asks you whether you want to run in parallel or serial.
- Runs in parallel.
- 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.