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- 1
- In a Terminal window, set your current directory as namd-tutorial-files using the cd command. Open a new session of VMD by typing vmd.
- 2
- Choose the File New Molecule... menu item of VMD. In the Molecule File Browser use the Browse... button to find the file ubq_ws.psf in the common directory. Load it by pressing the Load button. If you do not find the file, look for it in the common/example-output/ directory.
- 3
- In the VMD Main window your molecule should appear (ID 0).
- 4
- In the Molecule File Browser window, use the Browse... and the Load buttons load the file 1-2-sphere/ubq_ws_eq.restart.coor into your psf file. Be certain that the Load files for: field says 0:ubq_ws.psf. If you have not done that exercise, a copy of the corresponding output files is provided in the subdirectory 1-2-sphere/example-output/. When you are done, close the Molecule File Browser window.
Now you have the equilibrated ubiquitin in a water sphere loaded in VMD. The next step is to eliminate the water.
- 5
- In the VMD TkCon window, type the following commands:
set selprotein [atomselect top protein] |
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$selprotein writepdb common/ubq_ww_eq.pdb
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You have created a pdb file that contains the equilibrated protein without water.
- 6
- Delete the current molecule by selecting it in the VMD Main window and choosing the Molecule Delete Molecule menu item and keep VMD opened.
Next: Constant Velocity Pulling
Up: Steered Molecular Dynamics
Previous: Steered Molecular Dynamics
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