[gmx-users] Energy between desired selected molecules
Faezeh Pousaneh
fpoosaneh at gmail.com
Wed Jul 13 11:52:16 CEST 2016
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
> > >>>>>>>>>>
> > >>>>>>>>>> * 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
> > >>>>>>>>>>
> > >>>>>>>>>> * For (un)subscribe requests visit
> > >>>>>>>>>>
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > >>>>>>>>>>
> > >>>>>>>>>> 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!
> > >>>>>>>>>
> > >>>>>>>>> * Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>>>>
> > >>>>>>>>> * For (un)subscribe requests visit
> > >>>>>>>>>
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > >>>>>>>>> or
> > >>>>>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>> ==================================================
> > >>>>>>>
> > >>>>>>> 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
> > >>>>>>>
> > >>>>>>> * For (un)subscribe requests visit
> > >>>>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > >>>>>>> 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!
> > >>>>>>
> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>
> > >>>>>> * For (un)subscribe requests visit
> > >>>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> 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
> > >>>>
> > >>>> * For (un)subscribe requests visit
> > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>
> > >>>>
> > >> --
> > >> ==================================================
> > >>
> > >> 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
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list