[gmx-users] affect of water removal on subsequent energy calculations

[Alex]

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

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 <nedomacho at gmail.com<mailto:nedomacho at 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.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il><../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il<http://40weizmann.ac.il/>>
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> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at 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
>