Child pages
  • Mox_NAMD
Skip to end of metadata
Go to start of metadata

Below are the steps to install NAMD. Here abc is your userid and xyz is your group.

On your desktop or laptop:

(1) Go to below location:

(2) Click on the first link for Linux-x86_64-multicore .

(3) Register and then download the file name like below (The date time stamp will be different for your downloaded file.)


(4) Use sftp to copy the above file to your home directory on


    put NAMD_Git-2019-12-04_Linux-x86_64-multicore.tar.gz

On mox.hyak:

(1) ssh

(2) Get an interactive node:

srun -p xyz -A xyz --nodes=1 --ntasks-per-node=28 --time=2:00:00 --mem=100G --pty /bin/bash

(3) mkdir /gscratch/xyz/abc/namdinstall

(4) cp NAMD_Git-2019-12-04_Linux-x86_64-multicore.tar.gz /gscratch/xyz/abc/namdinstall

(5) tar -xvf NAMD_Git-2019-12-04_Linux-x86_64-multicore.tar.gz

(6) export PATH=/gscratch/xyz/abc/namdinstall/NAMD_Git-2019-12-04_Linux-x86_64-multicore:$PATH

(7) cd to the directory which has your NAMD configuration file.

(8) If name of your configuration file is ubq_ws_eq.conf then you can run namd2 as shown below:

     namd2 ubq_ws_eq.conf > ubq_ws_eq.log

  • No labels