[gmx-users] gmx potential and water

[André Farias de Moura]

hi Alex,

try this paper as a starting point:

David van der Spoel and Paul J. van Maaren: The origin of layer structure
artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11
(2006)

Andre

On Thu, Jul 21, 2016 at 11:07 PM, Alex <nedomacho at gmail.com> wrote:

> Hi all,
>
> What we have here is a well-equilibrated, well-behaved, 300 ns long
> simulation of an aqueous system (tip4p, ~50K atoms) at 300K and a version
> of gmx_potential.c hacked by one of our very well known members. It allows
> plotting potential in a all of the slices as functions of simulated time.
>
> I am looking at the time data produced by selecting just water as the
> contributing charge group. The value of epsilon is default. The result (for
> a given slice) is a massively noisy dataset, basically oscillations around
> zero, as one should expect. However, I have run this data through a very
> stringent lowpass filter (basically a recursive running average), so
> everything beyond a few hundred of MHz is gone. The filtered data features
> oscillations with a magnitude of, well, 0.5 V.
>
> Is this expected? Is this normal? Does it need more smoothing? Does it
> need rescaling by eps=80? I thought water should "self-screen" here...
> Also, there's a caveat: the trajectory is spit out every 50 ps (can't go
> finer, huge files), so it could be a classic case of aliasing. Any attempt
> at an explanation would be great. :)
>
> Thanks you,
>
> Alex
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090