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Molecular modelling tutorial

A live debian system could be installed onto a memory key. Please, provide me with a key and I 'll burn a copy for you. Booting from the memory key you can make few runs without modifying your computer or installing additional software. Otherwise check www.gromacs.org and install Gromacs on your computer.

In the home directory of the default user styliani you can find an example of MD run using Gromacs package.

Open a terminal window.

~$ cd teaching

Files in the example directory

c2h5oh.gro c2h5oh.pdb ethanol.mdp readme c2h5oh.itp ethanol.gro ethanol.top tutorial.html

Take a model from http://davapc1.bioch.dundee.ac.uk/prodrg/ Copy pdb and gromacs topology files. In the example c2h5oh.itp c2h5oh.pdb

Center molecule

~/teaching$ editconf -f c2h5oh.pdb -o c2h5oh.gro -box 1.5 1.5 1.5

Create simple model(provided) ethanol.top

Solvate it

~/teaching$ genbox -cp c2h5oh.gro -cs spc216.gro -o ethanol.gro -p ethanol.top

Setup simulation parameters ethanol.mdp

~/teaching$ grompp -f ethanol.mdp -c ethanol.gro -p ethanol.top

Run the smulations

~/teaching$ mdrun

See the results

~/teaching$ vmd -size 666 666 -f ethanol.gro traj.trr