Getting started - Methanol

VERSION 4.6
Sat 19 Jan 2013

Methanol

Now you are going to simulate 216 molecules of methanol 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 methanol molecules (.gro)
Topology file of methanol (.top)
Molecular Dynamics parameter file (.mdp)

Change your directory to tutor/methanol :

cd tutor/methanol

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

more conf.gro

Or to view the methanol box graphically:

rasmol methanol.pdb

The Carbon group (CH3) is treated as one particle. In the file it is called Me1 (methyl 1) and rasmol does not recognize it as carbon (and hence colors it purple).

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

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 "MeOH" (for methanol) or "System", which is the same for a box of methanol as we have. Select one and click OK. Then select Display->Animate from the menu. Use the buttons to see your methanol moving (note: "Play" steps one frame forward; "Fast Forward" plays; "Rewind" skips back to the beginning of the trajectory).

Analysis of the simulation

Calculate a radial distribution function of the oxygen atoms around oxygen atoms. The index file index.ndx now contains two groups, one with the methyl atoms and one with the oxygen atoms.

g_rdf -n index -o rdf-oo.xvg

The program will ask you for how many groups you want the calculate the RDF, answer 1 (and select oxygen and oxygen). Now, view the output graph.

xmgrace rdf-oo.xvg

Which shows you the radial distribution function for oxygen-oxygen in Methanol. Now do the same thing using the methyl group as reference and as target (and use e.g. rdf-mm.xvg as output file name). View all the graphs together:

xmgrace rdf-oo.xvg rdf-mm.xvg ../water/rdf.xvg -legend load

The xmgrace program will display three different graphs. Compare the resulting graphs. Explain the differences and the similarities.
We can also do a direct analysis of the number of hydrogen bonds in methanol, 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 methanol molecule? What is the maximum possible number? Compare the results to those from water
As a further test of the simulation we will compute the self diffusion constant of Methanol, again from the Mean square displacement (MSD) function.

g_msd -n index

(Select Me1, or O2). 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. Compare the result to water. Is it as you would expect?