[gmx-users] rerun under non-bonded E. terms

[Mark Abraham]

Hi,

Sorry, actually, that won't help you get non-bonded *forces* since there is
no way to decompose them. You can decompose energies that way. To get the
forces you want, you need a .tpr that has only non-bonded interactions, and
to do that correctly, you will have to explicitly list the [exclusions]
that would otherwise be generated by the bonds, as Justin suggests. See
chapter 5.

Mark

On Tue, May 12, 2015 at 3:39 PM Albert Solernou <a.solernou at leeds.ac.uk>
wrote:

> Thanks to you all,
> feel free to mark that question as "solved".
>
> Best,
> Albert
>
>
>
> On 05/12/2015 02:23 PM, Mark Abraham wrote:
> > Hi,
> >
> > Use the nonbonded terms in the .edr files, not the totals.
> >
> > Mark
> >
> > On Tue, May 12, 2015 at 2:32 PM Albert Solernou <a.solernou at leeds.ac.uk>
> > wrote:
> >
> >> Hi Mark,
> >> thanks for that. This was the route that I was taking so far. However,
> >> and I may be missing something, I don't see how your approach excludes
> >> the bonded terms from the -rerun calculation.
> >>
> >> Thanks,
> >> Albert
> >>
> >> On 05/12/2015 01:16 PM, Mark Abraham wrote:
> >>> Hi,
> >>>
> >>> This is one of the things for which mdrun -rerun on a subset trajectory
> >> is
> >>> useful. Make the subset trajectory, make the subset topology (including
> >>> keeping bonds plus their associated exclusions, as appropriate) and
> >> you'll
> >>> get the forces. tpbconv can make subsets, but YMMV.
> >>>
> >>> Mark
> >>>
> >>> On Tue, May 12, 2015 at 2:12 PM Albert Solernou <
> a.solernou at leeds.ac.uk>
> >>> wrote:
> >>>
> >>>> Hi,
> >>>> I may have not expressed well my final goal. I need a trajectory, a
> .trr
> >>>> file, that has the forces. I am interested in the non-bonded forces
> of a
> >>>> sub-set of the residues, so I need to re-compute these, and cannot use
> >>>> the values that come from the full trajectory where all the residues
> are
> >>>> present.
> >>>>
> >>>> Thanks for your time,
> >>>> Albert
> >>>>
> >>>> On 05/12/2015 12:59 PM, Justin Lemkul wrote:
> >>>>> On 5/12/15 7:57 AM, Albert Solernou wrote:
> >>>>>> Thanks Justin,
> >>>>>> still I would not know how to go from a .edr file into a trajectory
> >>>>>> that has the
> >>>>>> forces of the atoms I am interested in.
> >>>>>>
> >>>>> You don't.  The .edr file is the energy output of a simulation. If
> you
> >>>>> have your subtrajectory of interest, you'll get a new .edr file with
> >>>>> the quantities you want, if I understand your description.
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>>>> Best,
> >>>>>> Albert
> >>>>>>
> >>>>>>
> >>>>>> On 05/12/2015 12:48 PM, Justin Lemkul wrote:
> >>>>>>> On 5/12/15 7:46 AM, Albert Solernou wrote:
> >>>>>>>> Well, back to the beginning, then.
> >>>>>>>>
> >>>>>>>> Is there a way to do a re-run using only non-bonded energy terms?
> >>>>>>>> I'll explain a
> >>>>>>>> bit further. I have a trajectory, and want to get a
> (sub)trajectory
> >>>>>>>> that has
> >>>>>>>> only a sub-set of atoms and that accounts only for the non-bonded
> >>>>>>>> interactions
> >>>>>>>> within this sub-set of atoms. So far, I have the extracted
> temporary
> >>>>>>>> sub-trajectory that contains the solvent atoms as well as the
> >>>>>>>> residues I am
> >>>>>>>> interested in. Is there an easy way to do that? Or should I modify
> >>>>>>>> the source
> >>>>>>>> code, instead?
> >>>>>>>>
> >>>>>>> The nonbonded terms don't depend on the bonded terms; they are, by
> >>>>>>> default,
> >>>>>>> saved in the .edr file.  If you want some group-wise decomposition
> >>>>>>> (e.g.
> >>>>>>> interaction energy) then that's what energygrps are for. There is
> no
> >>>>>>> need to
> >>>>>>> modify code or hack the topology at all if this is what you're
> after.
> >>>>>>>
> >>>>>>> -Justin
> >>>>>>>
> >>>> --
> >>>> ---------------------------------
> >>>>      Dr Albert Solernou
> >>>>      EPSRC Research Fellow,
> >>>>      Department of Physics and Astronomy,
> >>>>      University of Leeds
> >>>>      Tel: +44 (0)1133 431451
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
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> >>>>
> >> --
> >> ---------------------------------
> >>     Dr Albert Solernou
> >>     EPSRC Research Fellow,
> >>     Department of Physics and Astronomy,
> >>     University of Leeds
> >>     Tel: +44 (0)1133 431451
> >>
> >> --
> >> Gromacs Users mailing list
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>
> --
> ---------------------------------
>    Dr Albert Solernou
>    EPSRC Research Fellow,
>    Department of Physics and Astronomy,
>    University of Leeds
>    Tel: +44 (0)1133 431451
>
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> Gromacs Users mailing list
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