Mark, Justin:
This is two against one, even though noone was questioning the
additivity of energy in forcefields with constant charges, etc.
So, let's go back specifically to solvation. Consider a system with two
oppositely charged ions (1 and 2) in water of your choosing (group 3).
For extreme simplicity, the ions are actually restrained at a distance R
from each other, and again for simplicity we're only interested in the
Coulomb part of the potential energy. The trajectory contains everything.
In one instance, we calculate E_tot - E_13 - E_23 - E_33, in another
E_12 (as one would easily do for a trajectory that has no water
coordinates). Are those two numbers in agreement and, if so, what is it?
q1*q2/R or q1*q2/eps/R?
Alex
On 4/11/2018 5:37 AM, Mark Abraham wrote:
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
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