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

[Mark Abraham]

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
>
> * 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.
>