NAMD Installer

1. Whats included in this installer ?

This installer script includes addition/update of the following tools;

  1. NAMD - Scalable Molecular Dynamics

2. Download NAMD

Download the “Linux-x86_64-multicore (64-bit Intel/AMD single node)” version of NAMD from this site : http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD

3. Download Installer

Download the installer script from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=70

4. Prepare for install

4.1. Make sure the NAMD downloaded .tar.gz file and the namdinstaller are in the same folder (your working directory… in the Downloads folder for example…)


4.2. Unzip the NAMD download file using the below command as example (in the shell terminal, in your working directory) ;

tar -xvzf NAMD_Git-2018-03-31_Linux-x86_64-multicore.tar.gz




4.3. Make ‘namdinstaller’ executable, using the below command;

sudo chmod 755 namdinstaller


5. How to run the installer?

Run the script with the following command as example, in your working directory. Specify the name of the unzipped namd folder, as shown below;

sudo ./namdinstaller NAMD_Git-2018-03-31_Linux-x86_64-multicore



After installation is complete, either log out of your machine and then log back in to start using the new updates OR run the following command in your terminal;

source /etc/profile.d/markcbm.sh

Make sure the installation worked, by executing the command ‘namd2’ in the terminal. The output should be similar to below, if the install is successful;


The setup assumes that you have not made any system level changes. If the install does not behave as expected, probably the system configuration has been changed. If you face any issues after this update, please let us know ASAP, so that we can help you troubleshoot the issue.

6. Issues ?

If you have any issues with running the installer or need any other information regarding this, please do not hesitate to contact us at contact at molbiocloud.com