Practical Session 11

Files for practical on 3/21/2013. These files will be available for the duration of the course.
[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory  -  
[   ]Argon_GMX.tar.gz2013-03-20 15:41 7.8K 
[DIR]SimulatingLiquidArgon/2013-03-20 20:41 -  
[   ]SimulatingliquidArgonwithGromacs.pdf2013-03-20 20:46 121K 
[   ]gromacs455_static_MacOSX_10.6.8.tgz2012-03-07 18:18 86M 
[DIR]src/2012-08-16 10:36 -  


Please open the LJ fluid in Gromacs Wiki on Blackboard (Navigate through Course Documents → Practicals →Practical 11 → LJ Fluid in Gromacs).

It has further instructions and you will create your own wiki page to store results from this session.


Gromacs is a very fast MD code that can be used for classical (and mixed QM/MM) MD simulations of biomolecules and other systems.

Install the precompiled distribution on your workstation:

curl -O
cd ~
tar -zxvf gromacs455_static_MacOSX_10.6.8.tgz

This unpacks the distribution into $HOME/opt. In order to run any of the Gromacs tools one needs to set up the Gromacs environment by running in the shell:

. ~/opt/bin/GMXRC

(This is called to source GMXRC because instead of the . command you could also use source.) Check that this worked by executing

mdrun -h

should give you the help information of the mdrun program.

Whenever you want to run Gromacs you have to source GMXRC at the beginning of your shell session. If you use multiple shells then you have to do it for each shell. GMXRC sets a number of environment variables that Gromacs requires to point to very specific places. You can look at the file ~/opt/bin/GMXRC.bash to see what happens.

Note that the GMXRC environment script expects to find everything under $HOME/opt. If you move the whole opt directory elsewhere then you need to manually change the opt/bin/GMXRC* files.

Compiling your own

The src directory contains the source code for Gromacs 4.5.5 and for FFTW 3.3.1 (fast fourier transform library) together with instructions how they can be compiled (file compiling.txt). These instructions should work for both Mac OS X (if the C compiler is installed) and Linux.


See notes on VMD from the previous session.