[gmx-users] Energy between desired selected molecules

Faezeh Pousaneh fpoosaneh at gmail.com
Fri Jul 1 16:20:55 CEST 2016 

Thank you again :)


Best regards


On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/1/16 10:05 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin and Mark for the help. I could obtain.
>>
>> More details for someone with similar question:
>>
>> 1- First I defined the molecules (resnr 1 to 4) I wanted to look at  (from
>> existing simulation: production.tpr  6000wat.gro) :
>>
>> g_select -f 6000wat.gro -s production.tpr -on index.ndx
>>
>> resnr 1 to 4
>>
>> resnr 5 to 6000
>>
>> (all other renaming molecules also must be defined as next group,
>> resnr 5 to 6000)
>>
>> 2- Then I looked at the name of groups created in the index file and
>> changed the current .mdp file to include those groups:
>>
>>
> For the sake of correctness in the archive, don't do this:
>
> tc-grps                   =  resnr_5_to_6000     resnr_1_to_4
>>
>
> For the purpose of a re-run, tc-grps being split this way has no effect.
> But one should absolutely not divide thermostatting groups in this way.
>
> I feel it is important to point out so that (1) people don't make this a
> common practice and (2) you don't start re-using .mdp files with these
> settings.
>
> This is all you need to accomplish what you want in terms of the energy:
>
> energygrps            =  resnr_5_to_6000    resnr_1_to_4
>>
>>
> The rest of the .mdp file should be the same as your original run.
>
> -Justin
>
>
> 3- Finally rerun
>>
>> grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
>> mdrun -rerun traj.xtc -s new.tpr -mn index.ndx
>>
>> 4- So, if you now run g_energy you'll find those specified groups
>> energies.
>>
>>
>>
>> Best regards
>>
>>
>> On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>>>
>>> Thank you both, I am close to solve it. The remaining problem is when I
>>>> mdrun -rerun, it tells the number of atoms in old trajectory is not the
>>>> same as chosen index file.
>>>>
>>>> Number of atoms in trajectory (24000) does not match the run input file
>>>>
>>>>>
>>>>> (16)
>>>>
>>>>
>>>> Your .tpr file needs to contain the same system that you ran before.
>>> The
>>> only thing that changes is the energygrps setting in the .mdp file.
>>>
>>> -Justin
>>>
>>>
>>> can you help me?
>>>
>>>> Best regards
>>>>
>>>>
>>>> On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>>>
>>>>> Yes as Justin says, a group is a few molecules that you selected :-)
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
>>>>>>
>>>>>> Thank you Mark, I see. But what is the solution then? The way you
>>>>>>>
>>>>>>> proposed
>>>>>>
>>>>>>
>>>>>>> ''You can make a new .tpr file with those
>>>>>>> energy groups and use mdrun -rerun on the old trajectory, however.''
>>>>>>>
>>>>>>>  is not my answer, since I do not want the energy for a ''group'' of
>>>>>>> molecules, rather for specified combination of few molecules I define
>>>>>>>
>>>>>>> from
>>>>>>
>>>>>> g_select.
>>>>>>>
>>>>>>>
>>>>>>> The only function available is to define energygrps in the .mdp file,
>>>>>> supply an
>>>>>> index file with those groups (e.g. from g_select) and do as Mark says
>>>>>> and
>>>>>> re-calculate those interaction energies with mdrun -rerun on the
>>>>>> existing
>>>>>> trajectory.  The short-range nonbonded interaction energies between
>>>>>> those
>>>>>> groups
>>>>>> will be written to their own terms in a new .edr file.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> Best regards
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
>>>>>>>
>>>>>>> mark.j.abraham at gmail.com>
>>>>>>
>>>>>
>>>>> wrote:
>>>>>>
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>>>
>>>>>>>> The .edr file contains only what was written during the simulation,
>>>>>>>>
>>>>>>>> and
>>>>>>>
>>>>>>
>>>>> that was for any energy groups defined before that run. You're trying
>>>>>>
>>>>>>>
>>>>>>>> to
>>>>>>>
>>>>>>
>>>>> ask it to make an arbitrary repartition, which it can't do unless it
>>>>>>
>>>>>>> recorded every component of the energy for every frame (which would
>>>>>>>>
>>>>>>>> take
>>>>>>>
>>>>>>
>>>>> forever and use lots of disk). You can make a new .tpr file with those
>>>>>>
>>>>>>> energy groups and use mdrun -rerun on the old trajectory, however.
>>>>>>>>
>>>>>>>> Mark
>>>>>>>>
>>>>>>>> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosaneh at gmail.com
>>>>>>>> >
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Does someone know how to obtain energy between specific molecules
>>>>>>>>> in
>>>>>>>>>
>>>>>>>>> the
>>>>>>>>
>>>>>>>
>>>>>> system?
>>>>>>>
>>>>>>>>
>>>>>>>>> What I did and seems not be correct is:
>>>>>>>>> 1- I obtained the molecules I wanted to look at:
>>>>>>>>> g_select_mpi -f 600gro.gro -s production.tpr -on
>>>>>>>>>
>>>>>>>>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
>>>>>>>>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
>>>>>>>>>
>>>>>>>>> 3- Finally put the created .tpr file as an input for g_energy
>>>>>>>>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s
>>>>>>>>> tpxout.tpr)
>>>>>>>>>
>>>>>>>>> But that is not the solution, since it gives energy for whole
>>>>>>>>> system.
>>>>>>>>> Best regards
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 629
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
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>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>> --
>>>>>>
>>>>> Gromacs Users mailing list
>>>>>
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>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>
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