Questions tagged [molecular-dynamics]

For questions related to the use of or theory behind classical or ab initio molecular dynamics.

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18
votes
3answers
704 views

What are the types of ab initio Molecular Dynamics?

I am new to the world of Molecular Dynamics, and am curious to know exactly what is considered to be an ab initio Molecular Dynamics (AIMD) method, and how do they work? The seminal work by Roberto ...
21
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5answers
2k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
16
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6answers
2k views

How do I simulate the interaction between two atoms?

I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
40
votes
4answers
800 views

How should one choose the time step in a molecular dynamics integration?

Choosing too small of a timestep leads to an unrealistic simulation time, whereas too big of a timestep leads to the system not being represented correctly (or, in the case of an algorithm like SHAKE, ...
15
votes
2answers
326 views

What are the parameters that need to be calculated to design the structure of a molecule?

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...
9
votes
1answer
138 views

What are the types of Quantum Molecular Dynamics (QMD)?

In similar spirit to recent questions on Quantum Monte Carlo, ab-initio Molecular Dynamics, types of SCF, and others, I would like to ask: What are the types of Quantum Molecular Dynamics (QMD)? As I ...
8
votes
1answer
74 views

How to calculate the volumetric energy density of a molecule?

I am trying to store hydrogen in a hydrocarbon. The example can be taken as cyclohexane ($\ce{C6H12}$) which is in a hydrogen-rich state. Its hydrogen-lean state is Benzene. I want to calculate the ...
12
votes
1answer
94 views

How can one computationally determine the flammability of a molecular system?

I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
13
votes
2answers
314 views

What are good resources to learn Materials Modeling?

I wonder if there are any books or resources to start learning Materials modelling using methods density functional theory quantum monte carlo molecular dynamics
9
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3answers
2k 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.
6
votes
0answers
116 views

How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
11
votes
1answer
344 views

Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
10
votes
1answer
455 views

How should I generate a radial distribution function (RDF) for an MD trajectory with python?

I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
10
votes
2answers
246 views

What are the factors to consider before docking 2 proteins?

With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
19
votes
2answers
767 views

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 ...
17
votes
1answer
179 views

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 ...
15
votes
1answer
2k views

How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
12
votes
1answer
96 views

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?
12
votes
1answer
128 views

Deviation caused by using DFT in Non-Adiabatic Molecular Dynamics

To calculate the excited state properties and processes of semiconductors (e.g. during the photocatalysis process), can be important. Non-Adiabatic Molecular Dynamics (NAMD) is one of the popular ...
12
votes
1answer
498 views

Compute RDF between COMs of two selections (or groups) using GROMACS

I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
11
votes
1answer
163 views

Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
10
votes
1answer
164 views

Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?

I wanted to understand the Free Energy Perturbation in an NVT ensemble. Wikipedia explains it as: $$ \tag{1} \Delta F = F_1 - F_0 = -\kappa T \ln \left<\exp\left( \frac{-(E_1-E_0)}{\kappa T}\right)...
10
votes
1answer
149 views

What is the "overcoherence problem" in Ehrenfest dynamics?

I am a novice in Ehrenfest dynamics and would like to know why Ehrenfest dynamics suffers from the "overcoherence problem"?
9
votes
2answers
680 views

How to calculate the computational time required for a MD simulation

I have a ligand and receptor to simulate with MD. These are my specs: Receptor has 4674 atoms, Ligand has 273 atoms CHARMM force field MD software GROMACS Computing machine: Amazon g4dn.xlarge (1 GPU ...
8
votes
2answers
338 views

Large pressure fluctuations in molecular dynamics

I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level. For example, I set the pressure at 1 bar and it averages ...
5
votes
3answers
142 views

How to make input script file for nanoparticle using LAMMPS?

Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...