Skip to main content

Questions tagged [monte-carlo]

For questions related to Monte Carlo methods, which solve deterministic numerical problems via a probabilistic sampling approach.

Filter by
Sorted by
Tagged with
3 votes
1 answer
88 views

Identification of all possible H adsorption sites on the surface

I want to calculate Gibbs free energy of hydrogen atom adsorbed on an adsorption site (ΔGH*), to evaluate the HER activity of that particular surface of material. How can i identify all possible H ...
Joyal sunny's user avatar
5 votes
1 answer
58 views

Does GROMACS have the capability to do Monte Carlo simulation of proteins?

My supervisor says that GROMACS can do both (all-atom) MD and MC simulations of proteins. I never found anything while searching the Internet about MC-only simulations. As far as I found, GROMACS can ...
user366312's user avatar
  • 2,546
2 votes
0 answers
33 views

How can I determine if a system is equilibrated?

Cross-posted in CrossValidated.SE and SCSE I am experimenting with a new MCMC protocol and new research. In the context of Monte Carlo simulation, a "state of equilibrium" refers to a ...
user366312's user avatar
  • 2,546
3 votes
0 answers
30 views

How can I compute the longest relaxation time?

Cross-posted on Stats.SE and on SciComp. In the case of Monte Carlo simulations: Autocorrelation Time ($\tau_{\text{int}}$): A measure of how many steps are needed for the correlations in the chain ...
user366312's user avatar
  • 2,546
2 votes
1 answer
232 views

Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics

Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
Rubi Agrawal's user avatar
5 votes
1 answer
135 views

Plot MSD (mean square displacement) versus time for a polymer chain

Cross-posted on Computational Science SE. The following are the movements of the center of mass of a polymer chain over time in a monte carlo simulation. ...
user366312's user avatar
  • 2,546
5 votes
1 answer
44 views

How to Balance Translational and Angular Maximum displacements in a Monte Carlo Simulation of Non-Spherically Symmetric Molecules?

I'm writing a computer simulation code to model a system of non-spherically symmetric molecules, meaning that their state are described by both angular and translational components. In typical Monte ...
Lodin Ellingsen's user avatar
1 vote
0 answers
53 views

Resource recommendation for learning matter modeling for a novice [closed]

I am a starting researcher in condensed matter physics. Hence, i have all the necessary background regarding quantum physics, and condensed matter physics. But what i want to do is to learn different ...
kal92's user avatar
  • 11
4 votes
2 answers
237 views

Thermodynamics: System versus Ensemble

In the context of thermodynamics, an ensemble is a hypothetical collection of identical copies of a system, each in a different state, used to represent the statistical behavior of the system. That ...
user366312's user avatar
  • 2,546
3 votes
1 answer
137 views

When should I use Charge-Charge Interactions, Charge-Dipole Interactions, and Dipole-Dipole Interactions in molecular simulation?

I used LJ-potential, Hard-sphere, Soft-sphere, Harmonic, Square-well, etc. potentials in the case of simulation of polymer movement. However, I never used Charge-Charge Interactions Charge-Dipole ...
user366312's user avatar
  • 2,546
6 votes
1 answer
126 views

Is the term "Forcefield" only reserved for MD (Molecular Dynamics)?

As far as I understand, there are two related concepts called potential and forcefield. A forcefield is essentially a sum term of more than one potential. My question is, is the term "Forcefield&...
user366312's user avatar
  • 2,546
2 votes
0 answers
66 views

Are lattice-based Monte Carlo simulations used in the case of liquids and gases?

The Ising model uses a lattice-based model as it is reasonable to simulate magnetic behavior in a solid. Is lattice-based Monte Carlo modeling used in the case of the simulation of gases and liquids (...
user366312's user avatar
  • 2,546
2 votes
0 answers
43 views

What factors determine the selection of a specific type of MC move?

There are several types of Monte Carlo (MC) moves that can be used in simulations: Metropolis-Hastings: a sampling technique used to generate a Markov chain of states with desired probabilities by ...
user366312's user avatar
  • 2,546
2 votes
0 answers
91 views

How to generate force-fields for RASPA2?

Just getting into RASPA (https://github.com/iRASPA/RASPA2). I need to generate forcefields, I would like to use UFF (Universal Force Field), how do I go about doing this?
Xavier Phillips's user avatar
2 votes
2 answers
140 views

What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?

What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
user366312's user avatar
  • 2,546
9 votes
2 answers
705 views

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
  • 2,034
3 votes
1 answer
128 views

Are MD and MC both parts of statistical physics?

Are MD (Molecular Dynamics) and MC (Monte Carlo) both parts of statistical physics or is only one of them? If so, which branch (e.g., mechanics, thermodynamics, etc.) and why?
user366312's user avatar
  • 2,546
5 votes
3 answers
311 views

Are MD and MC both able to study both equilibrium and non-equilibrium systems?

As far as I understand, a system in equilibrium is which already reached its equilibrium state. And, a non-equilibrium system is which hasn't reached its equilibrium state yet. Are MD (Molecular ...
user366312's user avatar
  • 2,546
4 votes
1 answer
40 views

Can you supply me with some book names on MC protein simulation?

Is there any book written on protein simulation specifically using the Monte Carlo technique (i.e., not QM or MD)? If so, can you supply me with some names of such books?
user366312's user avatar
  • 2,546
3 votes
0 answers
67 views

Partial atomic charge from lodwin charge - quantum espresso [closed]

Looking to calculate partial atomic charges for a GCMC calculation. I have relaxed a structure with QE. Projwfc.x gives Lodwin charge of a Ni(II) atom as; ...
Xavier Phillips's user avatar
4 votes
1 answer
51 views

Is RASPA2 a sensible Monte Carlo software to find adsorption sites within porous materials?

Looking to find sorption sites of species including (H2, CO2, and N2) within porous materials (metal-organic frameworks) for further DFT work. Is RASPA2 a sensible Monte Carlo software to achieve this?...
Xavier Phillips's user avatar
4 votes
1 answer
184 views

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 ...
Saha_1994's user avatar
  • 969
4 votes
2 answers
627 views

Python script for Metropolis Monte Carlo (global optimisation)

I have written a python script to do global optimisation on interatomic potential (IP) using Metropolis Monte Carlo. I have attached the part of the script which is the Metropolis MC part. I have ...
DGKang's user avatar
  • 900
2 votes
0 answers
57 views

how to incorporate size polydispersity in colloidal suspensions [closed]

Basically, I'm working on spherical colloids and investigating the phase behavior of these monodisperse colloids using Monte Carlo simulations (Fortran 77 coding). Now I want to introduce size ...
siva ram's user avatar
5 votes
1 answer
51 views

Generalization of always accepting box upscaling moves in Monte Carlo for a triclinic box

When you are using Monte Carlo scheme to simulate equilibrium phases of convex hard-core molecules, namely, whose energy is infinite when in contact and 0 otherwise in a standard, cubic simulation box,...
PKua's user avatar
  • 151
1 vote
1 answer
41 views

How do I initialize the lattice/grid in a Potts Model?

I am studying the Cellular Potts Model Tutorial. However, this doesn't say anything about the grid/lattice initialization. How do I initialize the lattice/grid in a Potts Model? I.e., how do I assign ...
user366312's user avatar
  • 2,546
3 votes
1 answer
31 views

How do I calculate the acceptance criterion for configuration bias sampling of my polymer?

I am running a lattice simulation of a single chain polymer on a lattice with every other site occupied by solvent. The additional wrinkle is that every particle on the lattice has a number/spin ...
megamence's user avatar
  • 4,171
6 votes
0 answers
46 views

How to rigorously prove the existence of a coil-globule transition of polymers in an on-lattice simulation? [closed]

I am running on-lattice simulations of polymers. I am testing out different Hamiltonians and testing different regimes to test if they yield interesting behavior. My question is, how do I rigorously ...
megamence's user avatar
  • 4,171
3 votes
0 answers
84 views

What are the similarities between MD and MC in the case of protein simulation? [closed]

As far as I understand, both MD and MC simulation methods use Force Fields. Are there any other similarities between them?
user366312's user avatar
  • 2,546
6 votes
0 answers
195 views

Regarding use of GCMC to add water molecules

I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
ansonthms's user avatar
  • 981
2 votes
1 answer
623 views

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 ...
user366312's user avatar
  • 2,546
3 votes
0 answers
130 views

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 ...
user366312's user avatar
  • 2,546
3 votes
1 answer
80 views

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 ...
user366312's user avatar
  • 2,546
4 votes
0 answers
62 views

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....
user366312's user avatar
  • 2,546
3 votes
1 answer
62 views

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}...
user366312's user avatar
  • 2,546
4 votes
0 answers
76 views

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, ...
user366312's user avatar
  • 2,546
1 vote
0 answers
70 views

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 ...
user366312's user avatar
  • 2,546
4 votes
0 answers
65 views

How to construct spinodal and binodal curves from a molecular simulation?

Pretty much what the title states: what is a procedure to construct a binodal and spinodal curve (temperature against composition)? I am running an on-lattice polymer solution Monte Carlo simulation ...
megamence's user avatar
  • 4,171
6 votes
1 answer
93 views

End-to-end correlation of polymers not decorrelating

I am running Monte Carlo simulations of polymers with nearest neighbor interactions only. For benchmarking purposes, I decided to run some excluded volume simulations (no overlaps) allowed on a 3D ...
megamence's user avatar
  • 4,171
9 votes
1 answer
136 views

Some questions about implementing Swendsen-Wang algorithm

I have a lattice system with two types of sites, namely A and B. Both A and B have a possible up or down spin orientation. There exists $J_\textrm{aa,align}/J_\textrm{aa,mis}$, $J_\textrm{bb,align}/...
megamence's user avatar
  • 4,171
12 votes
1 answer
185 views

Benchmarking Monte Carlo simulations of polymers

I have written a simulation engine in C++ to run a Monte Carlo simulation of polymers on a lattice. My code basically plants a polymer on a lattice, and performs certain Monte Carlo moves, including ...
megamence's user avatar
  • 4,171
8 votes
1 answer
107 views

How often does one have to run polymer Monte Carlo moves to effectively sample phase space?

I have a polymer and solvent on a lattice, and I am performing an NVT Monte Carlo simulation. I am performing the following moves on it: My question is, how should these moves be conducted to ...
megamence's user avatar
  • 4,171
14 votes
2 answers
794 views

How do you incorporate hydrogen bonding into molecular simulations?

How do computer simulations of liquid hydrogen-bonding systems incorporate hydrogen bonding? Since I think hydrogen bonding has mixed covalent and electrostatic character, wouldn't you need something ...
user avatar
4 votes
1 answer
63 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
megamence's user avatar
  • 4,171
4 votes
1 answer
98 views

Simulating polymers using cellular automata?

I am a physics student, and I am working on my final year project, I am planning to simulate polymers using cellular automata. I am really struggling with this project, if someone can give me any ...
omar karbal's user avatar
12 votes
1 answer
243 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
Squishy's user avatar
  • 123
11 votes
2 answers
396 views

Starting configuration for a molecular simulation

When doing a computer simulation, what’s the best way to prepare a starting configuration to avoid biasing your results? The book Computer Simulation of Liquids suggests putting the molecules on an ...
user avatar
9 votes
1 answer
575 views

Why is specific heat not zero at absolute zero?

In this old paper on Monte Carlo simulations of Lennard-Jones solid, specific heat behaviour (both $c_p$ and $c_v$) have been reported. As you can see from the picture below, both $c_p$ and $c_v$ goes ...
Magic_Number's user avatar
17 votes
3 answers
2k views

Is there a more efficient hard sphere packing algorithm?

I am trying to pack hard-spheres in a unit cubical box, such that these spheres cannot overlap on each other. This is being done in Python. I am given some packing fraction ...
megamence's user avatar
  • 4,171
12 votes
1 answer
496 views

Are there examples of ab initio predictions on small molecules without the "major approximations"?

In most textbooks the precise Schrödinger euqation of a molecule is given (and the "beautiful thing" stops here), then born oppenheimer approximation is made, then layers of other ...
jw_'s user avatar
  • 405