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Questions tagged [forcefields]

Questions related to forcefield development and use in matter modeling.

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37 votes
2 answers
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Machine learning interatomic potentials for molecular dynamic simulations: are they good?

I know the general question of machine learning in computational chemistry has been already raised here: What is the current status of machine learning applied to materials or molecular systems? ...
exsonic01's user avatar
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26 votes
1 answer
351 views

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
jheindel's user avatar
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22 votes
1 answer
262 views

Benchmarking data for Ewald summation algorithms

Are there good benchmarks available for testing homemade Ewald summation code? Optimally it would be very nice if there was several types of systems. NIST has a very nice benchmark for energies of ...
B. Kelly's user avatar
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18 votes
2 answers
2k views

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
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18 votes
1 answer
365 views

What are the advantages of (semi)-empirical force fields over Machine Learning Potentials?

I am currently working with ReaxFF, an empirical reactive force field that can describe chemical bond forming and breaking. The main advantage over ab initio methods are of course the greatly ...
lcdumort's user avatar
  • 283
17 votes
1 answer
350 views

Constructing a molecular polarizability tensor from sets of atomic polarizabilities?

Often empirical electrostatic models or molecular force fields approximate the molecular polarizability using an additive model, e.g., for N atoms: $$ \alpha_{mol} = \sum_i^N \alpha_{atom_i} $$ This ...
Geoff Hutchison's user avatar
16 votes
1 answer
128 views

Which modelling package currently implements an AI derived force field?

I would like to use an AI-derived force field as they seemed to have lesser computational cost. Which simulation package (Gromacs, Amber, NAMD...) currently implement some of them?
BND's user avatar
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14 votes
2 answers
994 views

Finding parameters for a molecule in various forcefields

Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...
megamence's user avatar
  • 4,171
14 votes
0 answers
108 views

Generating interatomic potentials via force matching [closed]

I am trying to learn best practices for force matching ab initio molecular dynamics (AIMD) data with nonlinear least-squares minimization to generate interatomic potentials for use in classical MD. I ...
anneb101's user avatar
  • 995
13 votes
3 answers
5k views

What does "force field" mean?

In MD simulations we often hear the term force field. What is it? We know, for example that, Gromacs provides various types of forcefields.
littleworth's user avatar
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13 votes
2 answers
570 views

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

This is a doubt regarding the usage of various forcefields together in MD simulation of hydrates. For Eg., we use TIP4P/ice for water molecules, OPLS-UA for methane and EPM2 for carbon dioxide and so ...
Kavya Mrudula's user avatar
13 votes
0 answers
552 views

Applicability of GFN-FF force field and other xTB methods for dynamics of ions in water [closed]

I am working on a project involving water clusters with ions in them. One of the problems that I ran into quite early on was that good forcefield parameters are not available for highly charged ions ...
S R Maiti's user avatar
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12 votes
3 answers
471 views

Limitations of pairwise additive forcefields

What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?
user avatar
12 votes
2 answers
334 views

What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?

I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
Marco Di Gennaro's user avatar
11 votes
1 answer
1k views

Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?

My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...
DLV's user avatar
  • 211
10 votes
2 answers
977 views

How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
Vranvs's user avatar
  • 423
10 votes
1 answer
109 views

What is the state-of-the-art in current flexible water models?

Do we have water models so far which are flexible? How good can they model specific properties of water and are they currently used with force fields and in actual simulations?
sycramore's user avatar
  • 273
10 votes
1 answer
240 views

Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?

I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein. There is a particular target for which AMDock Vina, with its default force fields, ...
Shredderroy's user avatar
10 votes
1 answer
329 views

Basics of numerical energy minimization techniques used in molecular dynamics?

The question below describes my plan to make a basic molecular dynamics calculation using a Python script rather than a canned, self-contained program. There seems to be three parts: a model of the ...
uhoh's user avatar
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9 votes
3 answers
544 views

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...
fred85's user avatar
  • 99
9 votes
1 answer
730 views

Where to get Tersoff and SW potentials for LAMMPS

I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
jboy's user avatar
  • 1,151
9 votes
1 answer
119 views

Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
Kavya Mrudula's user avatar
9 votes
0 answers
110 views

DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?

The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
uhoh's user avatar
  • 2,034
8 votes
1 answer
628 views

Alternative to CGenFF for generating large ligand topology

I am now preparing a ligand topology following GROMACS protein-ligand tutorial. However, I have a large ligand (446 atoms). $ wc -l my_ligand.pdb 446 my_ligand.pdb ...
littleworth's user avatar
  • 1,674
8 votes
1 answer
262 views

Parameterize a complex that contains Transition metal (Build Force Field)?

It is a general question. I know, but I need some help. I am interested to parametrize a complex that contains transition metal like Ru and Pt etc. Furthermore, I will use this Force Field to do ...
Abd-Elazeem Mohamed's user avatar
8 votes
1 answer
60 views

Attempts to define atomic energies based on electron density?

The concept of an atom in a molecule is undefined in quantum mechanics. Consequently, very useful properties like atomic charges, bond orders, and so on cannot be rigorously defined. There are many ...
jheindel's user avatar
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8 votes
0 answers
133 views

Calculate FF interaction energy of small molecular dimers [closed]

I have a set of molecular dimers (~25 atoms) for which DFT-D3 interaction energies are calculated by Psi4 and Turbomole program. Now I want to compare these values against Force-Field methods like UFF/...
Pro's user avatar
  • 1,024
8 votes
0 answers
352 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF [closed]

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
geo's user avatar
  • 455
7 votes
2 answers
410 views

What does it mean by "transferable" in the case of a force field?

According to Wikipedia: Functional forms and parameter sets have been defined by the developers of interatomic potentials and feature variable degrees of self-consistency and transferability. When ...
user366312's user avatar
  • 2,546
7 votes
1 answer
61 views

Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS

I am working on a project that requires generating a large dataset of Co3O4 and Fe3O4 structures under various temperatures and pressures using LAMMPS. The structures will be used for training machine ...
li jiwei's user avatar
7 votes
1 answer
255 views

How to go from Tinker parameter file to GROMACS topology file for improper and proper dihedrals?

I have been playing with a polymer called glyme, and I have run Tinker analyze on it to get OPLS-AA parameters for it. I have attached the output parameter file to this post. My question is, how do I ...
megamence's user avatar
  • 4,171
6 votes
2 answers
516 views

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

In classical molecular dynamics simulations of complex molecular systems, the force field (FF) contains information about bonded (bonds, angles, dihedrals and impropers) and non-bonded parameters. It ...
user35952's user avatar
  • 343
6 votes
2 answers
335 views

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
6 votes
1 answer
363 views

What software implements UFF

I am looking for common software packages that implement UFF ideally with an example of how to run it to calculate forces and energies. I see that Rdkit should be capable of doing this for example, ...
Tristan Maxson's user avatar
6 votes
1 answer
605 views

Where can I find/generate force-field parameters for common inorganic anions in water?

I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
S R Maiti's user avatar
  • 7,021
6 votes
1 answer
128 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
6 votes
1 answer
538 views

Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?

I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
S R Maiti's user avatar
  • 7,021
6 votes
0 answers
79 views

Simple code for polarizable force-field molecular dynamics? [closed]

I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple "toy repositories" for these models such as is ...
Wesley's user avatar
  • 1,040
6 votes
0 answers
257 views

How do I generate an aluminum force-field for a LAMMPS input file? [closed]

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
Shreyan Ghosh's user avatar
5 votes
1 answer
804 views

Why are Coulomb interactions modeled with just r, not r squared?

As far as I understand (as a complete beginner to molecular simulation and modelling), Coulomb's law for two atoms i and j is: $$F=k\frac{q_iq_j}{(r_{ij})^2}$$ (the force is proportional to the ...
Cro's user avatar
  • 51
5 votes
1 answer
178 views

Classical MD Simulation for mineralization process

I'm currently trying to simulate the calcium carbonate mineralization process on the surface of nanoparticles. In here, I've already borrowed the classical force-field parameters on here(https://pubs....
Arete's user avatar
  • 195
5 votes
1 answer
109 views

How to Derive the Kong-Chakrabarty Mixing Rules

Background In the world of atomistic modeling with classical force fields, one is often given a force field defined by like interactions (e.g. argon-argon interactions). If one is working with a ...
Hayden S's user avatar
  • 940
5 votes
1 answer
115 views

When and why are torques needed in molecular dynamics simulations?

I have seen that many MD simulations compute the torques due to dipole-dipole interactions and other interactions. I understand that there is a torque on a dipole in an electric field. I don't ...
jheindel's user avatar
  • 3,584
5 votes
1 answer
47 views

Forcefield parameterization techniques

Suppose I have a novel synthetic protein. I want to find the classical forcefields that accurately models the dynamics and thermodynamics of the protein. How do I do that?
Robin's user avatar
  • 61
5 votes
1 answer
87 views

Training a ML forcefield on a simple bulk material

Lately, I've become quite intrigued by the recent advances in machine learning forcefields within the field of computational chemistry. I've developed a curiosity about training a simple forcefield on ...
Okano's user avatar
  • 1,417
5 votes
1 answer
122 views

Where to find/ to get Tersoff and Stillinger Weber Potentials for MD simulation using LAMMPS

I'm trying to calculate the thermal properties of Silicene with hydrogen and halogen atoms. My problem is that, there's seems no available potential for Tersoff and Stillinger Weber Potential. and I'...
deee's user avatar
  • 129
5 votes
0 answers
78 views

Reference textbooks for calculating pressures/stress/strain/tensors? [closed]

Is there a good reference textbook for calculating pressures/stress/strain/tensors in materials - vapor, liquids and solids? Pure physics is fine, but it would be a bonus if it also included force-...
B. Kelly's user avatar
  • 4,376
4 votes
1 answer
361 views

What is the procedure to develop a new force field for molecular simulation?

Suppose, I want to develop a novel force field for proteins. What is the empirical procedure I should follow to do that?
user366312's user avatar
  • 2,546
4 votes
1 answer
73 views

Force field for charged peptide-ion system

I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
Arete's user avatar
  • 195
4 votes
1 answer
100 views

Advantages/Disadvantages of Qeq over Drude polarizable model?

For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach ...
Hemanth Haridas's user avatar