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

[Martin Kamp Jensen]

Hi Chris,

On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk
<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)."


>
> Good luck,
> Chris
>
> 2010/11/6 Martin Kamp Jensen <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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>
>
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Regards,
Martin.
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