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Subsections



Ubiquitin in a Water Box: Simulation with Periodic Boundary Conditions

In this section, you will examine the minimization and equilibration of ubiquitin in a water box with periodic boundary conditions.

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...nvironment than a water sphere surrounded by vacuum provides.}
\end{minipage} }


Configuration File

1
Go to your 1-3-box directory by typing cd ..\1-3-box. Here, you will find a configuration file for the minimization and equilibration of ubiquitin in a water box. All output files for the minimization and equilibration of your ubiquitin in a water box system will be placed in this directory.

2
Open the configuration file, ubq_wb_eq.conf using WordPad.

The configuration file contains some commands which are different than the water sphere configuration file. Here, these differences are pointed out and explained.

3
The only differences in this file lie in the ``Simulation Parameters" section, where three new categories of parameters have been added. The ``Output" section has also been modified. The new commands are listed:

Note that the commands which specify spherical boundary conditions have been completely removed, since this simulation is using periodic boundary conditions.

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...ntroduction of artifacts from an unstable starting structure.}
\end{minipage} }

Run your Simulation

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...ow:
\\ \\
{\tt namd2 ubq\_wb\_eq.conf > ubq\_wb\_eq.log \&}
}
\end{minipage} }

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...zation if your system is already equilibrated.}
\end{itemize}}
\end{minipage} }


next up previous
Next: Ubiquitin in Generalized Born Up: Basics of NAMD Previous: Ubiquitin in a Water
namd@ks.uiuc.edu