VMD

Description

VMD is a powerful molecular visualization tool that is very popular for preparation and analysis of biological systems (protiens, nucleic acids, etc.). VMD can be used to animate and analyze the trajectory of molecular dynamics (MD) simulations from both external MD programs and NAMD. NAMD is a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD.
Homepage: https://www.ks.uiuc.edu/Research/vmd

Access

Running VMD in the Portal

There are a variety of VMD modules supported on Terra and Grace.
It is suggested to run VMD using VNC implemented under Interactive Apps in the Portal. You will need to request a GPU node.
When the portal VNC terminal is started, use the following commands to launch VMD.

Grace

To purge unnecessary modules before getting started:

[ NetID@cluster ~]$ml purge

To load a particular version of VMD on Grace:

[ NetID@cluster ~]$ml iccifort/2020.1.217 impi/2019.7.217 VMD/1.9.3-Python-2.7.18

To launch VMD:

[ NetID@cluster ~]$vmd

Terra

To purge unnecessary modules before getting started:

[ NetID@cluster ~]$ml purge

To load a particular version of VMD on Terra:

[ NetID@cluster ~]$ml VMD/1.9.3-LINUXAMD64-opengl

To launch VMD:

[ NetID@cluster ~]$vglrun vmd