AMBER

Last Update: 27 Nov. 2024

AMBER is a modeling and molecular mechanics/dynamics simulation program package developed by Professor Coleman’s group at the University of California. Programs including builder modules for arranging solvent water molecules and fitting charges are available.


Available users

Kyushu Univ. users Academic users Non-academic users
OK OK NG

Site license (Kyushu University only)

Installation on equipments owned, leased, operated, or managed by Kyushu University in the applicable campuses:

Module

Module name Version
amber 24
amber-cuda 24-12.2.2
Refer to the following page for the usage of modules:
Module usage

Usage

Setup Environment

AMBER CPU

$ module load gcc
$ module load impi
$ module load amber

AMBER GPU

$ module load gcc
$ module load impi
$ module load cuda
$ module load amber-cuda

Execution

AMBER CPU

#!/bin/bash

#PJM -L rscgrp=a-batch
#PJM -L node=2
#PJM --mpi proc=240
#PJM -L elapse=2:00:00
#PJM -j

module load gcc
module load impi
module load amber

mpiexec -n $PJM_MPI_PROC pmemd.MPI -O -i mdin
  • 2 nodes and 240 processes
  • Loading an input file mdin
  • This is an example of pmemd parallel version. For other versions, please refer to the following.

sander serial version

mpiexec sander -O -i mdin

pmemd serial version

mpiexec pmemd -O -i mdin

sander parallel version

mpiexec -n $PJM_MPI_PROC sander.MPI -O -i mdin

AMBER GPU

#!/bin/bash

#PJM -L rscgrp=b-batch
#PJM -L node=1
#PJM --mpi proc=4
#PJM -L elapse=2:00:00
#PJM -j

module load gcc
module load impi
module load cuda
module load amber-cuda

mpirun -map-by ppr:4:node pmemd.cuda.MPI -O -i mdin
  • 1 node (exclusive use), 4 processes, and 4 GPUs.
  • Loading an input file mdin
  • An example of pmemd parallel version