All Questions
Tagged with intermolecular-forces molecular-dynamics
14 questions
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Resource estimate for ab initio calculation [closed]
I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”.
I have asked the authors the following naïve questions directly via email?
What was the ...
- 245
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Charge polarisation in acetamide molecule due to different lithium salts (varying anions)
I am trying to understand how will acetamide molecules behave in the presence of lithium salts with different anions (nitrate, bromide and perchlorate).
Among the three, it is evident that bromide is ...
- 111
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64
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How to model a molecule of benzene surrounded by 100 molecules of water with molecular dynamics?
I have experience calculating molecular properties (mostly DFT). However, I would like to spend some time on molecular dynamics methods. I would like to ask your advice to direct me towards a program ...
user55257
2
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1
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240
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Magnitude of Lennard-Jones force evaluated with molecular dynamics simulation
The intent is to evaluate the error source of a molecular dynamics (MD) simulation which is only based on the Lennard-Jones interaction between noble gases (helium in this case). What is the magnitude ...
- 43
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Pressure of a system of particles
I'll derive the pressure of a system of particles, which would be used in a MD simulation for example, according to Allen's Computer Simulation of Liquids and show where my issue is.
Consider a ...
- 111
4
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611
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Hessian Matrix and Physical directions: Potential Energy Surface
How do the eigenvectors of the Hessian Matrix for potential energy surface correspond directly to the physical directions of translation, rotation and vibration?
I see that they might correspond to ...
- 1,171
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3
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1k
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Why aren't the Anton computers used more widely?
The Anton computers are purpose-built by DE Shaw research for molecular dynamics simulations. They achieve performance up to an order of magnitude faster than can be achieved with commodity hardware, ...
- 438
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Is the 12-6 Lennard Jones potential a good description of van der Waals interaction energy?
It seems to me that the Lennard Jones potential oversimplifies the more complex nature of van der Waals forces. However, in most of the MD simulation package, this is generally accepted.
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Radial pair distribution function (VMD). How to define it for a water NaCl system with multiple Na and Cl?
I'm struggling to understand a paper in which someone has presented radial distribution functions (RDFs) for a system that contains multiple Na, Cl, and water atoms/molecules. I don't know exactly ...
- 73
2
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1
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110
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Understanding water models?
I generally work on fluid flow, so some basic concepts in chemistry are new to me.
Work I'm doing requires use of molecular dynamics (MD) to do classical potential simulations of water–NaCl systems ...
- 29
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61
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How can I define a torsion force field for $n$ points in space?
I would like to define a model for torsion force field between $n$ point in space.
I thought to generalize the OPLS model:
$$
\sum_\mathrm{dihedrals} \left( \frac {V_1} {2} \left [ 1 + \cos (\phi-\...
- 924
2
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1
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434
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Calculate force on atoms given the energy of configuration, trajectory of simulation and position of atoms in each frame
Background
I am using a neural network to calculate the potential energy of atoms in a configuration and then adding energy of all atoms to compare it with the true energy of the configuration(label) ...
- 460
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What is "time-dependent evolution of the complex noncovalent interaction networks" and why this is important?
From Maximilian Scheurer, Peter Rodenkirch, Marc Siggel, Rafael C. Bernardi, Klaus Schulten, Emad Tajkhorshid and Till Rudack Biophysical Journal, Volume 114, Issue 3, 577-583:
One of the most ...
- 924
1
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1
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Difference between Force Field and topology, and other related questions
I am performing some Molecular Dynamics computer simulations and I am learning about the various Force Fields (FF) such as OPLS-AA, OPLS-UA, AMBER, etc.
Many things are still unclear to me. I put ...
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