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Next: Ubiquitin in a Water Up: Basics of NAMD Previous: Solvating the Protein

Subsections


Ubiquitin in a Water Sphere: Simulation with Non-Periodic Boundary Conditions

In this section, you will examine the minimization and equilibration of ubiquitin in a water sphere placed in vacuum.


Configuration File

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...our file is correct before you submit a simulation to be run!}
\end{minipage} }

% latex2html id marker 4320
\fbox{
\begin{minipage}{.2\textwidth}
\includegra...
...hort on time, and examine the contents of this section later.}
\end{minipage} }

1
Go to your 1-2-sphere directory by typing cd ..\1-2-sphere. Here, you will find a configuration file for the minimization and equilibration of ubiquitin in a water sphere.

All output files for the minimization and equilibration of your ubiquitin in a water sphere system will be placed in this directory. The configuration file is the only input file placed here, since it is particular to this simulation. The pdb, psf, and parameter files, which may be used by many other simulations, are placed in your common directory and are called by each respective configuration file.

Open WordPad by clicking Start $\rightarrow$ Programs $\rightarrow$ Accessories $\rightarrow$ WordPad. Open the configuration file, ubq_ws_eq.conf in your 1-2-sphere directory.

The configuration file may seem complex at first, but it will be examined line by line to determine its function in your simulation.

Note that when ``#" appears at the beginning of a line, the entire line is treated as a comment and ignored by NAMD. In the middle of a line, ``;#" is used to comment out the remainder of the line.

2
The ``Job Description" section contains only comments, and its purpose is to inform those who view the configuration file about what it is meant for. Your comment should read

# Minimization and Equilibration of  
# Ubiquitin in a Water Sphere
 

3
The ``Adjustable Parameters" section contains five commands:

4
The ``Simulation Parameters" section contains many commands, commented into different categories:

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...ture. \textbf{A value of 1.0 is often a good starting point.}}
\end{minipage} }

\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...se water molecules have been parametrized as rigid molecules.}
\end{minipage} }

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
... simulations using
non-periodic or semi-periodic boundaries.}
\end{minipage} }

5
The ``Extra Parameters" section contains commands which are applicable to more specific simulations. Included here are commands which characterize the spherical boundary conditions on the water sphere. These conditions prevent the sphere from undergoing evaporation or diffusion.

6
The ``Execution Script" section contains three commands, the first two of which apply to minimization and the last one of which applies to equilibration.

7
Now, close the configuration file by clicking File $\rightarrow$ Exit.

% latex2html id marker 4604
\framebox[\textwidth]{
\begin{minipage}{.2\textwid...
...rent/ug/}{http://www.ks.uiuc.edu/Research/namd/current/ug/}}.}
\end{minipage} }

\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...owing: {\tt temperature, velocities,} or {\tt binvelocities}.}
\end{minipage} }

 


Run your Simulation

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

\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...are in, you
should be able to type {\tt namd2} and run it.
}
\end{minipage} }

Your simulation should take about 20 minutes to complete, and NAMD will produce the output files described in Section 1.7.


next up previous
Next: Ubiquitin in a Water Up: Basics of NAMD Previous: Solvating the Protein
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