GROMACS is a versatile package to perform molecular dynamics. OCTOPUS users can use it freely on OCTOPUS by the batch job.
 
GROMACS is undergoing trial service. Although support on "basic use" as described on this page is possible, technical support such as program tuning cannot be applied, so please understand.
 

How to use

GROMACS is permitted to use only for processing by batch job.
Below is an explanation for using GROMACS and an example of job script.
 
* Please refer to the manual in official site about GROMACS.
 

Making a job script

The following example is a job script to execute GROMACS in 48 processes (using 2 nodes, 24 processes per node).

 
The installation directory of GROMACS is:

/octfs/apl/GROMACS/2016.1/

For various input files of GROMACS, please visit official site .
 
A description of the other lines of the job script is here.
 

Submitting a job script

Input the created job script by "qsub" command.

% qsub gromacs.sh

When the execution is completed, the calculation result is output to the result file.
 

How to use with GPU

In OCTOPUS, GROMACS can also be used with GPU. The version of GROMACS for GPU execution is 2016.5, and the version of CUDA is 9.0.
 
Below is an explanation for using GROMACS with GPU and an example of a job script.
* Please refer to the manual in official site about GROMACS.
 

Making a job script

The following example is a job script to execute GROMACS in 48 processes with GPU (using 2 nodes, 24 processes and 4 GPUs per node).
 

 

The installation directory of GROMACS is:

/octfs/apl/GROMACS/2016.5_GPU/

For various input files of GROMACS, please visit official site .
 
A description of the other lines of the job script is here.
 

Submitting a job script

Input the created job script by "qsub" command.

% qsub gromacs.sh

When the execution is completed, the calculation result is output to the result file.