Questions tagged [molecular-mechanics]

Refers to the modeling of molecular systems with classical mechanics (e.g. Hooke's Law).

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How to choose between Molecular Dynamics and Monte Carlo when beginning to simulate either equilibrium or non-equilibrium systems?

Answers to Are MD and MC both able to study both equilibrium and non-equilibrium systems? include lots of examples pointing to "yes". I'm currently faced with a task of modelings small ...
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Using LAMMPS and VMD to analyze a new structure [closed]

I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape ...
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Mixed Solvent MD using OpenMM [closed]

I switched to using OpenMM recently and have got up and running without too much of a learning curve. My general workflow is as follows, using a cloud based GPU to actually run the simulation: ...
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Re-parametrization of force fields in LAMMPS [closed]

I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
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Building a script to automatically save .xyz format files from geometry optimization with AMMP in VegaZZ [closed]

I'm totally new to programming and computational chemistry. I'm using Vega ZZ as a free software to compute geometry optimization via MM (AMMP) in order to optimize the geometry of the found minima ...
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7 votes
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Is it incorrect to use a NVT ensemble for Non-equilibrium MD simulation?

I am getting some conflicting results on this topic while searching for literature online, so I am asking this question here with respect to a simplified experimental setup. If we are trying to ...
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Why can MD simulations not handle "exotic" materials?

We are all aware of the fact that MD Simulations using force fields can treat very big systems. But they cannot handle "exotic" materials. Why?
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Symmetry-preserving low-level structural relaxation

I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
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The number of long-range interaction pairs in Tinker

I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input. ...
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Is this statement correct: "All structural variations are energy driven"? [closed]

In modelling using molecular mechanics can one state that "all structural variations are energy driven?". The statement is related to protein-ligand binding in modelling. Sometimes one can ...
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Empirically determining thermostat damping factor

Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
geo's user avatar
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How to calculate the nuclear energy derivatives in molecular mechanics?

In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g. $V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
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Does increasing Lennard-Jones cutoff means higher accuracy?

I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
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What is the cutting edge for open-source Force-Field generation?

The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions ...
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Rule-of-thumb for Morse potential cutoff in molecular dynamics?

Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
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What are the main mathematical approaches to materials modeling? [closed]

What are the main mathematical approaches to materials modeling? This can include both analytical (closed-form) and numerical techniques.
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In molecular mechanics, how are van der Waals forces modelled?

In terms of energy, how are van der Waals forces modelled (are there formulas/laws that govern these)?
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