[gmx-users] Using mdrun -rerun to get energy values
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Nov 7 02:54:30 CET 2010
On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
> Hi Chris,
>
> On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
> <mitomaster at gmail.com <mailto:mitomaster at 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 :-(
I've fixed the code so that -rerun and EM or NM integrators flag a fatal
error.
Mark
>
> Good luck,
> Chris
>
> 2010/11/6 Martin Kamp Jensen <martin.kamp.jensen at gmail.com
> <mailto:martin.kamp.jensen at 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.
>
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>
> Regards,
> Martin.
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