[gmx-users] Energy between desired selected molecules

Justin Lemkul jalemkul at vt.edu
Fri Jul 1 16:17:20 CEST 2016 


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
>>>>>>>> --
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>>>>
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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
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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
>>
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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

==================================================

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