Questions tagged [water]
For modeling of H2O or H2O clusters.
18
questions
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1
answer
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Exclusion of Lennard-Jones potential between O-H and H-H in water models
In reading Jorgensen's 1983 paper comparing the properties of 6 water models it was mentioned that there is the inclusion of an L-J potential between pairs of oxygen molecules, but no mention of ...
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What is the gold standard ab initio pair-potential between two water molecules?
There are a myriad of pair potentials available for simulating the interactions between water molecules, ranging from simpler models like the SPC/E to more sophisticated ones based on high-level ...
3
votes
1
answer
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Order Parameter for Water in an MD Trajectory: Understanding Changes in Oxygen-Oxygen-Oxygen Triplet Angular Distributions
I'm interested in understanding how changes in the oxygen-oxygen-oxygen (O-O-O) triplet angular distribution can provide insights into the order parameter.
In literature, the tetrahedral order ...
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6
votes
1
answer
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Clustering Algorithms with Periodic Boundary Conditions
I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species.
Specifically, I am looking for clustering ...
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3
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1
answer
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Visualising the spatial distribution of water structure using VMD
I am trying to recreate Fig. 5b of this paper
I have a solvated NH4+ in my system and would like to create a similar visualisation for my case.
Can this be generated using VMD? If so could someone ...
1
vote
0
answers
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Temperature damping parameter in lammps [closed]
I need help on how to set Tdamping in MD simulation. In Lammps documentation it is mentioned that the typical value is 100 for nvt, but when I put this value to my ...
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votes
1
answer
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Adding water molecules to a system in LAMMPS
I have a LAMMPS data file with roughly 1000 water molecules, with constituent atoms defined by an atom type (i.e, OW = type 1, HW = type 2), while the molecule itself is not defined explicitly. ...
9
votes
2
answers
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Why are ions in water not paired?
This question is about ions in water, both in reality and as handled by MD (explicit solvent) and QM methods (eg AIMD). Basically the question is this: why are ions not always paired?
For a back of ...
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votes
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Is hexaamminecobalt(III) chloride thermodynamically stable in pure water?
It is often said that "while cobalt(III) per se is strongly oxidising, hexamminecobalt(III) chloride is stable, even in concentrated hydrochloric acid, due to the strong donor properties of the ...
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votes
1
answer
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Simulating autoionization of small molecules using DFT or AIMD
From what I'm reading, simulation of auto-ionization in liquid substances is hard to do using gas phase DFT or AIMD [1][2][3]. I am using ORCA to do my work and I must confess that I'm shocked to see ...
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How may I define the pressures of two sides of a membrane in Materials Studio? [closed]
To study SiO2, polyamide and two-layer SiO2-polyamide as the membranes in the reverse osmosis desalination of saline water; I used the Materials Studio software to model the systems. My question is:
...
13
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Applicability of GFN-FF force field and other xTB methods for dynamics of ions in water [closed]
I am working on a project involving water clusters with ions in them. One of the problems that I ran into quite early on was that good forcefield parameters are not available for highly charged ions ...
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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 ...
- 2,262
10
votes
0
answers
380
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Setup for 4-point flexible water model [closed]
I tried to search online if there are examples or suggestions on how to set up a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc., but there's no clear example ...
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7
votes
1
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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 ...
- 1,894
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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 ...
- 2,262
6
votes
1
answer
150
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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. ...
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answer
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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?
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