Questions tagged [molecular-mechanics]

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

Filter by
Sorted by
Tagged with
9 votes
2 answers

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 ...
uhoh's user avatar
  • 1,904
4 votes
0 answers

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 ...
daqureshi's user avatar
8 votes
0 answers

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: ...
NotEvans.'s user avatar
  • 181
2 votes
0 answers

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 ...
Paul Logan's user avatar
3 votes
0 answers

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 ...
user avatar
7 votes
1 answer

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 ...
mykd's user avatar
  • 2,282
12 votes
2 answers

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?
Pranoy Ray's user avatar
  • 1,611
6 votes
2 answers

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)...
David CY's user avatar
  • 271
7 votes
1 answer

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. ...
Patche's user avatar
  • 400
6 votes
0 answers

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 ...
BND's user avatar
  • 1,341
17 votes
1 answer

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
  • 445
9 votes
2 answers

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 -\...
Cody Aldaz's user avatar
  • 7,997
20 votes
2 answers

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 ...
mykd's user avatar
  • 2,282
18 votes
2 answers

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 ...
B. Kelly's user avatar
  • 4,326
12 votes
1 answer

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?
anneb101's user avatar
  • 985
8 votes
0 answers

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.
Peter Morgan's user avatar
  • 1,473
36 votes
3 answers

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)?
TheSimpliFire's user avatar