Hello, 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 ( http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html and http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html): 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 em.mdp. pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx << EOF 1 1 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 Regards, Martin.
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