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

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Wed Apr 11 11:51:56 CEST 2018


Ok, thanks for the advice,


On 11 Apr 2018, at 11:21 AM, Alex <nedomacho at gmail.com<mailto:nedomacho at 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.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
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