Questions tagged [atomistic-simulation]
The atomistic-simulation tag has no usage guidance.
36
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What are some ways to check if a molecular simulation is running properly?
Suppose, I am running a simulation of protein folding.
What are some techniques, methods, or intuitions that help me to understand whether a simulation is running properly, i.e., it is producing the ...
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What are some symptoms that could tell me that my simulation is not running properly?
Suppose, I am running a Monte Carlo simulation of protein folding using harmonic potential, function.
The inner loop of Monte Carlo has 100 iterations, and the outer loop has 1000 iterations.
What are ...
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3
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1
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Layer detection in a crystal structure
Context
I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
- 306
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What is the purpose of a kinetically resolved activation barrier in cluster-based kinetic Monte Carlo simulations?
I read several papers regarding the use of cluster-based kinetic Monte Carlo (kMC) simulations
They mention the need to use a kinetically resolved activation barrier by averaging over the forward and ...
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NPT Molecular dynamics calculation problem
I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem?
This is my code for the heating part. However, the ...
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What do we simulate with molecular simulation of proteins in the theoretical research?
I know that the following can be simulated:
secondary/tertiary structure prediction
protein-surface/protein-protein interaction tests
protein-ligand binding test
I wonder if references or ...
- 1,686
4
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Understanding use of Machine Learning in Multiscale Enhanced Sampling
Multiscale Enhanced Sampling Using Machine Learning
Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the ...
- 31.6k
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Restraining a specific bond in eABF simulations in NAMD?
I am currently running eABF(adaptive biasing) simulation using NAMD. I need to restrain a few terminal C-H bonds in the system. I tried including the additional definition for bond constraints in the ...
- 1,686
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simulate liquid solvent mobility through gel polymer electrolyte
I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such system?
Is MD a ...
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2
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What is the relationship between periodic boundary and the simulation box?
Suppose, the size of my simulation box is:
Width = 200
Height = 100
Where,
Top-left corner = (0, 0)
Bottom-right corner = (200,100)
Center of the coordinate is at (100, 50)
What would be the size ...
- 14.7k
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Effect of System Configuration on MD simulation results
Does System Configuration on which we run MD simulation (to obtain a trajectory for the system under investigation) affects the analysis results.
If it does, then could anybody explain me to what ...
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Av. pressure in NPT equilibration of highly concentrated system [closed]
I'm relatively new to MD simulation, and am studying a highly viscous system of very concentrated aqueous biphasic systems of two different electrolytes. The higher-concentration systems are ...
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How is temperature changes implemented in a molecular dynamics simulation?
I copied my question to this community as the advice of a user on Physics SE
MD simulations are always associated with a temperature that represents the natural state of a system.
However, some ...
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How to get started modeling liquid crystals?
I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
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Perform energy minimization of multiple models of protein-dna complexes
Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)?
I know of GROMACS or Chimera or the online servers but is ...
- 31.6k
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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?
During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
- 31.6k
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What does it mean by a "site" in the case of a CG model?
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
What does it mean by a "site" in the case of a coarse-grained (CG)...
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1
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Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins?
Examples will be highly appreciated.
Also, please, back them up ...
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Can protein modeling and simulation be used in developing a marketable product? [closed]
As we all know computer science, electrical engineering, etc. knowledge can be used in developing software and electronics/electrical products that can be sold to end-users (B2C).
Can protein modeling ...
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Interlink among different length scales of simulation and modelling techniques [closed]
I found this figure:
In the following paper:
A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites
However, I am skeptical about its correctness, as this paper is not peer-...
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Molecular MC simulation is not equilibrating [closed]
Suppose, a polymer has N monomers in its chain. I want to simulate its movement using the bead-spring model.
So, I wrote the following program in Python.
Polymer chain simulation with Monte Carlo ...
- 1,759
2
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1
answer
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Why do we even need periodic boundary conditions?
According to Wikipedia -
Periodic boundary conditions (PBCs) are a set of boundary conditions that are often chosen for approximating a large (infinite) system by using a small part called a unit ...
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What formula should I use to calculate the total energy of a linear polymer chain?
I am using the Bead-spring model to model a polymer chain.
Suppose, the polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
And,
I can use the following formula to calculate the total Lennard-Jones ...
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Where should I apply the harmonic spring function in the case of polymer simulation? [closed]
I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion....
- 1,759
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1
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How should I calculate total potential in a polymer chain?
Suppose, a polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
When calculating total LJ potential, do I need to calculate like this:
$$E(r_{12})+E(r_{23})+E(r_{31})$$
Or, do I calculate: $$E(r_{12}...
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What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]
As far as I understand:
Pruning means deleting something.
Enrich means to enhance/increase weight.
Now my question is, in the case of pruned-enriched Rosenbluth method (PERM):
For pruning/enriching, ...
- 14.7k
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0
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Polymer simulation [closed]
I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others.
Can anyone tell me what are the differences between the following three ...
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How to calculate the surface area of a stepped surface slab in a unit cell? [closed]
I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
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Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?
Slater type orbitals (STO) are considered to be more accurate than gaussian type orbitals (GTO) for atomic and molecular QM calculations because - among other reasons - they decay with $e^{-\alpha r}$ ...
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In which theoretical framework does the size of an atom depend on the temperature of the gas (Bose-Einstein condensates)
In order to pose the question, I reproduce an excerpt from this Physics.SE question, about the size of atoms in a Bose-Einstein condensate (BEC):
Heisenberg's uncertainty principle in frames of ...
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How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
I adapted an example first-principles water simulation to do simulations of liquid SiO2, but did not know what I was doing and did not remove a Grimme dispersion correction term.
It would be great to ...
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Are there any codes to study magnetic materials?
I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are:
Vampire: For the calculation of curie temperature via ...
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What are the more efficient, or easier, methods of handling electromagnetic interactions?
Since metals, metalloids, non-metals, and composites, have differing characteristics, plug-and-play methods, so to speak, would be useful.
Also, as it’s well known that a moving electrical field ...
5
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elastic constants transformation/basis change P21/a -> P21/n
I just calculated the stiffness tensor for a given material (a monoclinic molecular crystal)
using molecular simulation. When trying to compare my results to published experimental results
I found ...
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How to calculate the exchange matrix of a bilayer magentic system?
I have been using the Vampire atomistic simulation software for a while and it has a useful simulation for predicting the curie temperature. But in order to do that I need the exchange matrix of Co-...
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