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

[Mark Abraham]

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
> >>
> >> --
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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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