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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Harry M. Greenblatt
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