[gmx-users] Energy between desired selected molecules

Faezeh Pousaneh fpoosaneh at gmail.com
Wed Jul 13 09:59:08 CEST 2016 

Dear Justin,

I have a question regarding my last question (below which was 'obtaining
energy for different selections').

My selection is a molecule within specific z of the box. I want the
selected z remains fix for whole energy calculation. I realized that mdrun
-rerun does not update the position of the selection for all frames.
Therefore, I guess one needs first to make a 'dynamic' selection from
g_select. The resulted index file then contains  selections for all frames
written frame by frame. Now, I suppose one can go for mdrun -rerun with the
given index file. However, my question now is how properly re-name the
energy groups in .mdp file according to the index file which has so many
frames?

Thank you for help.

Best regards


On Fri, Jul 1, 2016 at 4:20 PM, Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
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>>>>>>>>>> before
>>>>>>>>>> posting!
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>>>>>>>>>>
>>>>>>>>>> or
>>>>>>>>>
>>>>>>>>
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
>>>>>>>>> * Please search the archive at
>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>>> posting!
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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!
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>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
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>>>>>> posting!
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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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>>>>
>>>>
>> --
>> ==================================================
>>
>> 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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>>
>
>

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