[gmx-users] Energy between desired selected molecules
Mark Abraham
mark.j.abraham at gmail.com
Wed Jul 13 12:16:16 CEST 2016
Hi,
Then you need two selections from each input frame, and to use trjconv to
make the output frame contain one selection and then the other, and then
new .mdp inputs that know that the atoms corresponding to the first
selection is this energy group and likewise the second.
Mark
On Wed, Jul 13, 2016 at 11:52 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:
> Many thanks Mark. I am sorry I need more help:
>
>
> If you're selecting different molecules for different frames, then simple
> > mdrun -rerun can't cope, because the energy groups are constant over the
> > rerun. Probably you want something like
> >
> > make a tpr that will evaluate the energy for each pair (e.g. with tpbconv
> > and a static selection in an index group)
>
>
> I see only one group can be selected here. right? then how the mdrun -rerun
> produces energy between different groups?
>
> >
>
> for each frame of the trajectory
> > make dynamic selection
> > use selection to get molecule subset of frame via trjconv
> > use mdrun -rerun with the above tpr and the subset of the frame
> >
>
> Should I change the energy group names in in original .mpd file according
> to the above first step before this mdrun?
>
> >
> > Mark
> >
> > On Wed, Jul 13, 2016 at 9:59 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
> > wrote:
> >
> > > 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
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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
> > > >>>>>>>
> > > >>>>>>> ==================================================
> > > >>>>>>> --
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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
> > > >>>>
> > > >>>> ==================================================
> > > >>>> --
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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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