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Removing Water Molecules

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...water
should be in principle avoided when doing simulations.}
\end{minipage} }

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.

\fbox{
\begin{minipage}{.17\textwidth}
\includegraphics[width=2.0 cm, height=2...
...ry by using the {\tt cd} command in the VMD command terminal.}
\end{minipage} }

2
Choose the File $\rightarrow$ 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]  
$selprotein writepdb common/ubq_ww_eq.pdb
 

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 $\rightarrow$ Delete Molecule menu item and keep VMD opened.


next up previous
Next: Constant Velocity Pulling Up: Steered Molecular Dynamics Previous: Steered Molecular Dynamics
namd@ks.uiuc.edu