Questions tagged [forcefields]
Questions related to forcefield development and use in matter modeling.
58
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Include Li+ in force field for Molecular Dynamics
I want to perform some MD including Li+ ions. Specifically I am interested in Li-TFSI (aka Lithium bis(trifluoromethanesulfonyl)imide).
I tested both the ATB repository and LigParGen and neither can ...
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1
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112
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How to pre-optimize metal-organic complexes in RDKit using UFF?
I have run into a particular problem while trying to automate my input file generation for ORCA calculations. Apparently, I either do not fully understand how SMILES strings work, or I am demanding ...
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Reference textbooks for calculating pressures/stress/strain/tensors?
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-...
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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 ...
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6
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2
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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 ...
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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&...
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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 ...
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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?
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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....
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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 ...
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13
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3
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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.
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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 ...
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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 ...
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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 ...
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How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?
I asked this at Biostars but the post seems to have been deleted there.
My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
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17
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1
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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 ...
- 9,045
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Rotational invariance of anisotropic polarization models
After writing out this question, I actually figured out the answer, but I am surprised I haven't seen this detail mentioned in almost any paper on the topic, so I will answer my own question here in ...
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0
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What causes atoms to not interact in LAMMPS? [closed]
I am trying to set up a LAMMPS simulation for depositing graphene on a nickel substrate. I am using ReaxFF forcefield. However, the carbon atoms just pass through the nickel atoms. Can anyone help me ...
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How can we test the force field (parameter) for a complex?
I built a force field for a complex. How can I check if the force field is working well or no?
I did a short molecular dynamics using AMBER only for the complex using the parameters I built. It worked ...
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0
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How do I put two forcefields in the same LAMMPS code? [closed]
I need to put two interactions of ffields in the same code, but, I don't know what is the problem with the way I tried it. The code shows me ...
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2
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Re-parametrization of force fields in LAMMPS
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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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'...
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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 ...
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Creating Amber/CHARMM style force field potential for energetic materials using DFT [duplicate]
What are the basic steps and methodologies used in creating inter-atomic force field potential for CHARMM/Amber style for energetic materials with the help of DFT? What are the best possible free ...
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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 ...
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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, ...
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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 ...
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Gromacs generate forces using .pdb topol.top and .mdp file [closed]
Given the start configuration (.pdb), topology file (topol.top) and run file(water.mdp).
I want to generate the forces on atoms. I tried, using:
...
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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 ...
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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 ...
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16
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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 ...
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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 ...
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6
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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 ...
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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
...
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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/...
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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. ...
- 33.6k
12
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3
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402
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Limitations of pairwise additive forcefields
What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?
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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 ...
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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 ...
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2
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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 ...
- 15.2k
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1
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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 ...
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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, ...
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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 ...
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12
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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 ...
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3
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Missing residues in ATB downloaded pdb/rtp files
I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md)
Two files are available: a PDB file and a topology ITP/RTP file.
The name of the ...
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26
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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 ...
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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 ...
- 6,591
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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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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 ...
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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?
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