Getting started - Water Main Table of Contents

VERSION 4.6 Sat 19 Jan 2013

Water

• Initial structure of a box of 216 water molecules (.gro)
• Topology file of water (.top)
• Molecular Dynamics parameter file (.mdp)

Change your directory to tutor/water :

cd tutor/water

Let's first have a look at the coordinate file:

more conf.gro

Or to view the water box graphically:

rasmol spc216.pdb

Have a look at the topology file:

more topol.top

Have a look at the MD-parameters file:

more grompp.mdp

Since all the neccesary files are available, we are going to preprocess the input files to create a run input (.tpr) file. This run input file is the only input file for the MD-program mdrun.

grompp -v

The run input file is only viewable with the program gmxdump. In this way it is possible to check if the preprocessor grompp worked well. The output may seem rather cryptic, so don't panic when you don't understand every single item in it.

gmxdump -s topol.tpr | more

Now it's time to start the simulation of 20 picoseconds.

mdrun -v

After the MD simulation is finished, it is possible to view the trajectory with the ngmx program:

ngmx

When the program starts, you must select a group of atoms to view. In our case that will be "SOL" (for solvent) or "System", which is the same for a box of water as we have. Select one and click OK. Then select Display->Animate from the menu. Use the buttons to see your water moving (note: "Play" steps one frame forward; "Fast Forward" plays; "Rewind" skips back to the beginning of the trajectory).

Analysis of the simulation

1. Calculate a radial distribution function of the Oxygen atoms. The index file index.ndx contains one group with all the oxygen atoms.
   
   

   g_rdf -n index

   
   The program will ask you for how many groups you want the calculate the RDF, answer 1. Now, view the output graph of g_rdf. The file is already prepared to produce a nice graph in the xmgrace program.
   
   

   xmgrace rdf.xvg

   
   Which shows you the radial distribution function for Oxygen-Oxygen in SPC water. The first peak is at roughly 0.28 nm, and has a height of 2.8. This means that the relative density of oxygen atoms in water, is almost 3 times higher at a distance of 0.28 nm from another oxygen atom. Obviously this is due to strong hydrogen bonding in liquid water.

2. We can also do a direct analysis of the number of hydrogen bonds in liquid water, based on O-O distance and O-H ... O angle.
   
   

   g_hbond

   
   Select twice 0, when asked. Check the output with
   
   

   xmgrace hbnum.xvg

   
   What is the number of hydrogen bonds per water molecule? What is the maximum possible number?

3. As a further test of the simulation we will compute the self diffusion constant of water. This can be computed from the Mean square displacement (MSD) function. The MSD determines how much on average a molecule has moved with time. After a certain time period there is no correlation between the starting position and the current position and the square displacement will be linear with time. The slope of the MSD function is the linearly proportional to the self diffusion constant.
   
   

   g_msd -n index

   
   View the output
   
   

   xmgrace msd.xvg

   
   Check that the graph is roughly linear. The g_msd program also computes the diffusion constant D for you. The experimental value is roughly 2.3 x 10^-5 cm²/s. The simulation result is clearly too high, due to the simplicity of the model.