Building Gramicidin A

Overview

These web pages are intended to walk you through the stages of setting up and equilibrating a molecular dynamics simulation. The system you will be working with is Gramicidin A (GA) embedded in a POPE membrane, surrounded by water. The final system should contain about 4300 atoms, making it reasonably small and easy to work with, but the nonhomogeneous nature of the system (protein + water + membrane) should make setting everything up a nontrivial and hopefully interesting process.

Disclaimer: The steps described here are not to be construed as the One True Way to set up MD simulations. Experienced simulators may very well take issue with the rough-and-ready way in which we prepare the system. Feel free to use this tutorial as a starting point for exploring new ways to set up and assemble the system.

General directions: Each web page is a step in the process of assembling a Gramicidin A system. The top portion of each page provides a discussion and motivation for that step. This is followed by links for "Run this step!" and "Continue" and a listing of the actual script which will be run by VMD. You should read the script to understand what it is doing before running it and continuing to the next step.

Special directions: Manual intervention is required in order to place the protein among the lipids. This step can't be fully automated, so you'll need to manipulate the coordinates using the mouse in VMD. Once you're satisfied with the position of the protein, save the position of the protein by continuing to and running the next step.

Good luck!

Starting VMD with this tutorial

This tutorial has been developed and tested with VMD 1.7.1 and NAMD 2.5b1. Later versions of VMD and NAMD should work, although VMD 1.7.2 (Windows only) will not work as it is missing the critical psfgen component. Earlier versions will probably not work.

There is a bug in the solvate 1.1, included with VMD 1.7.1 and 1.7.2, that results in extra angle terms being generated for water molecules when solvate is run after another topology file is loaded into psfgen. This can be avoided by running the water generation step in a separate VMD (which is, unforunately, incompatible with the web format of this tutorial, and therefore the bug was present in this example). This is fixed in solvate 1.2, with future versions of VMD.

As a workaround, this tutorial temporarily downloads solvate 1.1.1, which works correctly but does not require the newer version of psfgen used by solvate 1.2. You may download and install this plugin permanently by downloading and unpacking one of solvate-1-1-1.tar.gz or solvate-1-1-1.zip or in VMD's plugins/noarch/tcl directory.

In order to avoid the errors and frustration of typing commands manually, this tutorial links your web browser to a web server running inside VMD. Details on how this is done are available here. There are two recommended ways to start VMD with this tutorial:

The elegant but dangerous and somewhat painful way

  1. Configure your brownser to use VMD for chemical/x-vmd by following these directions. This can be painful.
  2. Follow this link to control.vmd to launch VMD with the tutorial. Quite elegant.
  3. Unless your browser asks you before launching VMD, turn this off so you don't accidentally download and execute a malicious Tcl script. Very dangerous!

The quick and dirty way

  1. Launch VMD manually.
  2. Copy and paste the following into the VMD text console:
      eval [::http::data [::http::geturl http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/control.vmd]]
Either way, you should have a running VMD and many lines about files being downloaded should have scrolled past on the console. The "Run this step!" links on this and the following pages should now work.

Skip to the simulation section!

Run this step!     Continue 

view_protein.vmd

# STEP 0: View Protein

# Load the PDB file
mol delete all

# mol load pdb input/1JNO.pdb
mol load pdb 1JNO.pdb