VMD設定

$ pbc set {100 100 100}
$ pbc box_draw -shiftcenterrel {0 0 0}

$ pbc box -on
$ pbc unwrap

參考
https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

VMD User's Guidehttps://www.ks.uiuc.edu/Research/vmd/current/ug/

python
$ import os
$ os.system('vmd conf.gro')
參考
https://www.ks.uiuc.edu/Research/vmd/current/ug/node246.html

Working with a Single Moleculehttps://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html#sec:LoadMol

Molecular Modeling

http://videominecraft.ru/watch/hChPzoEXK2Q/molecular-modeling.html

Creating high quality figureshttp://videominecraft.ru/watch/w5lq57JOf1o/vmd-creating-high-quality-figures.html

Distance Measurementshttp://videominecraft.ru/watch/QV0_CJHBF6U/distance-measurements-in-vmd.html

Solvating a Protein Using VMD

http://videominecraft.ru/watch/kIenedhCUQ8/solvating-a-protein-using-vmd.html

Rendering Images in VMD Using Tachyon, POV-Ray, Snapshot in Windows

http://videominecraft.ru/watch/wJo3zjRAQoo/rendering-images-in-vmd-using-tachyon-pov-ray-snapshot-in-windows.html

Creating representations and trajectory smoothing

http://videominecraft.ru/watch/dxB__iHZbWI/creating-representations-and-trajectory-smoothing-in-vmd.html

Loading a Trajectory

http://videominecraft.ru/watch/J1sMUjlT3kQ/loading-a-trajectory-in-vmd.html

making tutorial

http://videominecraft.ru/watch/ip7lmmD7Z2k/vmd-image-making-tutorial.html