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

[Krzysztof Mlynarczyk]

Hi Martin,

Well, I was browsing the source code just yesterday cause I also noticed
that with steep integrator mdrun does not notice -rerun presence. And it
turned out that in do_steep() no one cares if -rerun is on. And if you think
for a moment what it does, it makes sense. However, it would be good to add
a check in the future releases so that gmx_fatal() is called in case someone
combines -rerun with integrators from minimize.c.

I'm happy that I was helpful.

Chris

2010/11/6 Martin Kamp Jensen <martin.kamp.jensen at gmail.com>

> 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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