A simple coupled potential QM/MM/MD simulation.

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

Using VMD with AMBER - SECTION 6

By Ross Walker

Updated for VMD 1.9.2
^{[by Aditi Munshi and Ross Walker]}

6) Visualizing AMBER trajectories

Note: Unfortunately VMD cannot yet load compressed (gzipped) trajectory files so when you download the nc.gz files I provide here you will have to unzip then using gunzip before loading them into VMD.

Lets start by loading some trajectory files covering the first 10ps of a molecular dynamics simulation of the TRPCage extended structure shown above. These simulations were run using Sander v8.0.

Here are the files you will need: TRPcage.prmtop (128 kb), heat1.nc.gz (510 kb), heat2.nc.gz (515 kb)

Start by decompressing the two trajectory files:

>gunzip heat*.nc.gz

If VMD is running, quit it. This way we should be starting from the same point. Load VMD and browse for the TRPcage.prmtop file. Select AMBER7 Parm and hit Load. Into this structure we will load the two trajectory files, one after the other. So, load the first one, browse for heat1.nc and then choose "AMBER Coordinates" as the type and hit Load.

Note: There are two types related to Amber trajectory (nc) files. These are "AMBER Coordinates" and "AMBER Coordinates with Periodic Box". The difference between the two concerns whether the trajectory file is from a gas phase/implicit solvent/solvent cap simulation (AMBER Coordinates) or from a periodic simulation (AMBER Coordinates with Periodic Box). When sander writes an nc file from a simulation run with periodic boundaries, it writes an extra 3 floating point numbers to the end of each frame which are the box size. VMD is not smart enough to work out what type of trajectory file it is, so we need to tell it. In this case we have an implicit solvent calculation so select "AMBER Coordinates". You can often tell if you have selected the wrong format because things will look very weird. Feel free to try it. If you do load a simulation that looks strange, try deleting the molecule and reloading it, selecting the other format:


Last frame of heat1.nc loaded with "crd"	Last frame of heat1.nc loaded with "crdbox"

If it loads correctly, you should see the TRPcage structure appear in the OpenGL window and start to move. Next click Browse again and find heat2.nc. Load this in the same way (you don't need to reload the prmtop file). Make sure TRPcage.prmtop is selected in the "Load files for:" box. This will append the frames in heat2 to the frames we have already loaded. In this way, you can load a number of different trajectory sets into a single animation so that you can watch the full trajectory without interruption. You should now have 400 frames of TRPcage loaded. This covers 10ps of heating from 0K to 100K. Try replaying the trajectory. You can use the movie controls in the "VMD Main" window for this:

CLICK HERE TO GO TO SECTION 7