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

[Martin Kamp Jensen]

Hi Mark,

On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham <Mark.Abraham at 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 <
> 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 :-(
>

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.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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Regards,
Martin.
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