Hi Mark, On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote: > > Hi Chris, > > On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk < > mitomas...@gmail.com> wrote: > >> Hi, >> >> You need to use md integrator for -rerun to work. >> > > Aha, now it seems to work. Thanks! > > I am just sad that I did not find that information. According to > http://manual.gromacs.org/current/online/mdrun.html "With -rerun an input > trajectory can be given for which forces and energies will be > (re)calculated. Neighbor searching will be performed for every frame, unless > nstlist is zero (see the .mdp file)." > > > Writing and documenting bulletproof software is tough work :-( > Yes, sure - and GROMACS is not exactly a small toolset :-) > > I've fixed the code so that -rerun and EM or NM integrators flag a fatal > error. > Great! > > Mark > > > > >> >> 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 >> > > 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 > Regards, Martin.
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