SW:VMD
VMD
Contents
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