BS”D

Ok, thanks for the advice,


Harry


On 11 Apr 2018, at 11:21 AM, Alex 
<nedoma...@gmail.com<mailto:nedoma...@gmail.com>> 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

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.



--------------------------------------------------------------------
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

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