Questions tagged [water]

For modeling of H2O or H2O clusters.

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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria

My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
7
votes
0answers
75 views

Setup for 4-point flexible water model

I tried to search online if there are examples or suggestions on how to setup a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc. but there's no clear example on ...
6
votes
1answer
61 views

How to obtain electron charge density per unit volume about a water molecule using SlowQuant?

@Nike Dattani's answer to How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python recommends SlowQuant. I've used the install instructions for Linux on my ...
7
votes
0answers
59 views

How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab initio MD methods as shown in the figure below: The main aim is to recreate figure (a) via averaging MD configurations ...
6
votes
1answer
91 views

Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

I'm looking for a simulation of different water models (TIP3P, SPC/E, TIP4P, water models with flexible bounds) where the differences in simulation speeds on a common architecture are really seen. ...
9
votes
1answer
61 views

What is the state-of-the-art in current flexible water models?

Do we have water models so far which are flexible? How good can they model specific properties of water and are they currently used with force fields and in actual simulations?