Getting started - Water

| ## Getting started - Water Main Table of Contents | VERSION 4.0 Sun 18 Jan 2009

## Water

Now you are going to simulate 216 molecules of SPC water (Berendsen et al., 1981) in a cubic box. In this example the GROMACS software team already generated most of the neccesary input files. The files needed in this example are:

- 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.

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