[gmx-users] Energy between desired selected molecules
Faezeh Pousaneh
fpoosaneh at gmail.com
Fri Jul 1 16:06:04 CEST 2016
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:
tc-grps = resnr_5_to_6000 resnr_1_to_4
energygrps = resnr_5_to_6000 resnr_1_to_4
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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>>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
>
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