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Next: Output: Water Sphere Log Up: Basics of NAMD Previous: Ubiquitin in a Water

Subsections



Ubiquitin in Generalized Born Implicit Solvent

In this section, you will examine the minimization and equilibration of ubiquitin in generalized Born implicit solvent (GBIS).

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...of not modeling the solvent as accurately as explicit models.}
\end{minipage} }

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...n employing implicit solvent for molecular dynamics research.}
\end{minipage} }

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...n as well as the geometric mean of the two atoms' Born radii.}
\end{minipage} }

Configuration File

1
Go to your 1-4-gbis directory by typing cd ..\1-4-gbis. Here, you will find a configuration file for the minimization and equilibration of ubiquitin in implicit solvent. All output files for simulation of your ubiquitin in implicit solvent will be placed in this directory.

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

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

3
Because there is currently no way of calculating long-range interactions in implicit solvent, such as through PME, features based on periodic boundary conditions are not used with GBIS as listed below.

4
A few additional commands are required for implicit solvent use. The new commands are listed:

\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...cules nor ions should be included in the simulated structure.}
\end{minipage} }

Run your Simulation

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

Your implicit solvent simulations should take roughly the same time as the water sphere simulation. The simulation will produce output files similar to the ubiquitin in water sphere simulation, which are discussed in Section 1.7.


next up previous
Next: Output: Water Sphere Log Up: Basics of NAMD Previous: Ubiquitin in a Water
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