Hi,

What Justin said, plus the observation that you should know how you plan to
analyze the results before you run the simulation. In this case, that means
knowing what you'll learn from rerun energies. Sometimes this means that
you won't ever run the simulations, and those are the really efficient ones
;-)

Mark

On Wed, Apr 11, 2018 at 1:29 PM Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/11/18 4:21 AM, Alex wrote:
> > Screening effects in Gromacs come in a rather non-straightforward
> > manner in terms of data extraction: they certainly exist within the
> > simulations in the form of the fields induced by local water
> > orientation, but to extract them from reruns is extremely challenging
> > even if you're outputting water trajectories. If this is about
> > interactions between different parts of proteins, I would absolutely
> > output water trajectories, because otherwise you're left with
> > LJ+electrostatics and assumptions on local dielectric constant, which
> > in itself is a very nuanced problem:
> > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.077801
> >
>
> The reality isn't this complex for fixed-charge, additive force fields.
> The fundamental truth of a pairwise additive potential is that in a
> mixture of A+B+C, then the interaction energy of A-B in a given
> configuration does not depend in any way on C. So if C=water, then you
> should get the exact same interaction energy from a fully solvated or a
> fully desolvated system. This is not true when multibody terms are
> involved (polarizable force fields or actual, physical reality) but for
> the simple purpose of computing interaction energies, the waters are
> irrelevant.
>
> That said, unless the force field has been parametrized in a way that
> makes interaction energies physical valid or useful, the quantity itself
> means very little.
>
> -Justin
>
> > We're faced with very similar challenges at the moment, so we're
> > independently postprocessing complete trajectories (including
> > everything) and solving Poisson's eqn all over again to give e.g.
> > time-averaged 3D electrostatics maps.
> >
> > Alex
> >
> >
> > On 4/11/2018 1:56 AM, Harry Mark Greenblatt wrote:
> >> BS”D
> >>
> >>   Dear Alex,
> >>
> >>    Not *explicitly* related to water:  we would like to look at
> >> interaction energies between parts of proteins, or proteins and DNA.
> >> So screening comes to mind…
> >>
> >>
> >> Harry
> >>
> >>
> >> On 11 Apr 2018, at 10:51 AM, Alex
> >> <nedoma...@gmail.com<mailto:nedoma...@gmail.com>> wrote:
> >>
> >> If you plan to extract anything explicitly related to water from your
> >> reruns -- very much so. Basically unusable trajectories.
> >>
> >> Alex
> >>
> >>
> >> On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote:
> >> B”SD
> >>
> >> In an effort to reduce the size of output xtc files of simulations of
> >> large systems, we thought of saving these files without water molecules.
> >>
> >>    It occurred to us, however, that upon subsequent cpu-only reruns
> >> in order to do energy calculations, these results would be adversely
> >> affected, since the water molecules are not stored in the xtc file.
> >>
> >> Is this indeed a concern?
> >>
> >> Thanks
> >>
> >> Harry
> >>
> >>
> >>
> >> --------------------------------------------------------------------
> >> Harry M. Greenblatt
> >> Associate Staff Scientist
> >> Dept of Structural Biology
> >> harry.greenbl...@weizmann.ac.il<mailto:harry.greenbl...@weizmann.ac.il
> ><../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%
> 40weizmann.ac.il<http://40weizmann.ac.il/>>
> >> Weizmann Institute of Science        Phone:  972-8-934-6340
> >> 234 Herzl St.                        Facsimile:   972-8-934-3361
> >> Rehovot, 7610001
> >> Israel
> >>
> >>
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> >>
> >> --------------------------------------------------------------------
> >> Harry M. Greenblatt
> >> Associate Staff Scientist
> >> Dept of Structural Biology
> >> harry.greenbl...@weizmann.ac.il
> <../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%
> 40weizmann.ac.il>
> >> Weizmann Institute of Science        Phone:  972-8-934-6340
> >> 234 Herzl St.                        Facsimile:   972-8-934-3361
> >> Rehovot, 7610001
> >> Israel
> >>
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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