[gmx-users] Using mdrun -rerun to get energy values

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Sat Nov 6 17:49:14 CET 2010


Hopefully someone can help me understand how to use the mdrun -rerun
functionality, because currently I am confused. I would like to be able to
look up potential energy values for a number of conformations by calling
mdrun -rerun once.

The idea to use mdrun -rerun is from advice given to me by Mark Abraham on
the gmx-developers list (

You want GROMACS to find the energy of a potentially infinite set of
> coordinates that appear magically, and that is what mdrun -rerun does.

> The elegant way to do that is to write your series of conformations to a
> pseudo-trajectory (in whichever of GROMACS many trajectory formats is
> convenient to you), and then invoke mdrun -rerun on that trajectory with a
> suitable .tpr. Then you either parse the .log file or the output .edr file
> for the energies.

I wanted to find out how this works so I have been experimenting. I started
out by looking at the Peptide tutorial at
http://manual.gromacs.org/current/online/speptide.html. I used three
different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
three conformations and their energy values. For testing purposes I then
wanted to get the energy values for those three conformations using mdrun
-rerun (and since I already have the correct energy values it is easy to
verify the results).

First, I created a trajectory by concatenating the three conformations (gro
files) into one gro file (which is okay according to
http://manual.gromacs.org/current/online/gro.html: "gro files can be used as
trajectory by simply concatenating files"). I then used an mdp file with
integrator = steep and nsteps = 0 indicating that I just want the energy
value (listed in the output, in the log file or by using g_energy). Now, by
using mdrun -s <tpr file> -rerun <gro trajectory file> I only get the energy
value for the first conformation listed in the gro file used to create the
tpr file. The -rerun option does not seem to have any effect at all.

I used the following commands three times to create three different
conformations (one conf_mdrun.gro file for each time) with different energy
values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in

pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF




> editconf -f conf_pdb2gmx -o conf_editconf -d 0.5

> genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox

mv top_pdb2gmx.top top_genbox.top

mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top

> grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp

> mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun

I was hoping the following would give me the three energy values for the
three conformations in 2+1+0.gro, which is the concatenation of the three
conf_mdrun.gro files from before. However, I just get the energy value from
the first conformation in the file. Using the -rerun option does not make a
difference (I can put whatever after -rerun, even files that do not exist,
without any effect).

grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp

> mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro

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