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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:

https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD

(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.)

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

(4) Use sftp to copy the above file to your home directory on mox.hyak.uw.edu

    sftp abc@mox.hyak.uw.edu

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


On mox.hyak:

(1) ssh abc@mox.hyak.uw.edu

(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


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