Hi, You need to use md integrator for -rerun to work.
Good luck, Chris 2010/11/6 Martin Kamp Jensen <martin.kamp.jen...@gmail.com> > 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. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
