Questions tagged [water]

For modeling of H2O or H2O clusters.

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How does dimer and monomer zero point energy affect dissociation energy?

This paper by Xinchuan Huang et al. gives a calculation for the dissociation energy of a water dimer. The electronic dissociation energy (what they call $D_e$) is around 21 kJ/mol, and this is ...
Alex I's user avatar
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3 votes
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 ...
KashmirWalla's user avatar
3 votes
1 answer
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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 ...
Lodin Ellingsen's user avatar
3 votes
1 answer
142 views

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 ...
Saha_1994's user avatar
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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 ...
Saha_1994's user avatar
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4 votes
2 answers
180 views

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 ...
Priyanshu Gupta's user avatar
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 ...
Fryad Sharif's user avatar
4 votes
1 answer
598 views

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. ...
cultured_left_foot's user avatar
9 votes
2 answers
697 views

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 ...
Alex I's user avatar
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3 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 ...
Kanghun Kim's user avatar
7 votes
1 answer
276 views

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 ...
HCSthe2nd's user avatar
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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: ...
Khadijeh Kalateh's user avatar
13 votes
0 answers
486 views

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 ...
S R Maiti's user avatar
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7 votes
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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 ...
mykd's user avatar
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10 votes
0 answers
426 views

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 ...
mykd's user avatar
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7 votes
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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 ...
uhoh's user avatar
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8 votes
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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 ...
mykd's user avatar
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6 votes
1 answer
154 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. ...
sycramore's user avatar
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10 votes
1 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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