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12 votes
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Why are ions in water not paired?

There actually is ion pairing in aqueous solutions, but the concentration of paired ions is usually much lower than fully dissociated ions. You should also take into account that typical ...
Stephen's user avatar
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12 votes
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Simulating autoionization of small molecules using DFT or AIMD

This is because autoionization is very thermodynamically unfavored near room temperature. I don't know much about water in a water-DMSO mixture, but let's take pure water as an example. The ...
wzkchem5's user avatar
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9 votes
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What is the state-of-the-art in current flexible water models?

Allow me to begin with a disclaimer: what you have asked is a very contentious question among people who work on water models. I think much more contentious than it should be. Not necessarily because ...
jheindel's user avatar
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9 votes
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How to obtain electron charge density per unit volume about a water molecule using SlowQuant?

Firstly regarding the SlowQuant problems: In the version of SlowQuant you are using, the program takes two files as input. The molecules file with the coordinates, number of electrons, and atom IDs. ...
Erik Kjellgren's user avatar
8 votes
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Clustering Algorithms with Periodic Boundary Conditions

First, there is a recent paper in which they proposed a k-means clustering algorithm adapted for periodic boundary conditions. Their Python implementation is available here. However, the clustering ...
Shaun Han's user avatar
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6 votes
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Order Parameter for Water in an MD Trajectory: Understanding Changes in Oxygen-Oxygen-Oxygen Triplet Angular Distributions

While there are a number of order parameters which can track the phase transitions and other physio-chemical changes, what you are asking here is about the tetrahedral orientational factor (OTO) which ...
mykd's user avatar
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5 votes
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Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

You may be able to find some bounds on performance such as O(n3) based on the number of water molecules etc, but honestly benchmarks not performed on your own hardware are always somewhat hard to use ...
Tristan Maxson's user avatar
4 votes
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Exclusion of Lennard-Jones potential between O-H and H-H in water models

The original publications may give some reason for omitting HH and OH Lennard-Jones terms -- but my first assumption would certainly be computational simplicity. Having said that, these models are ...
Shern Ren Tee's user avatar
4 votes
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What is the gold standard ab initio pair-potential between two water molecules?

I'm not an expert, but I believe Paesani's many-body MBPol force fields Acc. Chem. Res. 49, 1844 (2016) afford some of the most accurate descriptions of the interactions between water molecules. The ...
Susi Lehtola's user avatar
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3 votes
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Is hexaamminecobalt(III) chloride thermodynamically stable in pure water?

I think it is tricky to do the analysis in "pure water", since you cannot have a charged solution. Maybe what you mean is an aqueous solution at neutral pH? Based on what I saw in the ...
Stephen's user avatar
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3 votes
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Visualising the spatial distribution of water structure using VMD

The figure that you have provided depicts the spatial distribution of water molecules around the NH$_4$$^+$ ion. This is generally generated by calculating the 3D probability density of water-O atoms ...
Hemanth Haridas's user avatar
3 votes

Adding water molecules to a system in LAMMPS

Here's what I would do in your situation: Replicate the box three times (replicate 3 1 1 let's say) Use region to define the &...
Shern Ren Tee's user avatar
2 votes

Why are ions in water not paired?

It's the entropy – suggested reading, ET Jaynes: Information theory and statistical mechanics. For the same reason, water vapour exists already at room temperatur (~1 mol/m³, TU Wien: Vapor Pressure ...
Rainald62's user avatar
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1 vote

Visualising the spatial distribution of water structure using VMD

VIAMD software will allow you to do that. You can use the sdf function in the script editor after loading your trajectory. It would like something like that depending on your topology: ...
mathieu linares's user avatar

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