Questions tagged [molecular-dynamics]

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

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3
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0answers
11 views

Proper normalization of the radial distribution function to take into account unlike pairs only

In calculating a radial distribution function for a simulation for a few thousand molecules, I loop over unlike pairs and calculate the radial distribution function with respect to a particular site ...
4
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0answers
28 views

Define stress-strain for a multi-wall carbon nanotubes bundle

I want to simulate a MWCNT bundle in which the central MWCNT is pulled out of the bundle. How to define the stress/strain curve of such system? I am building my system with scikit-nano and using ...
4
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0answers
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Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS?

I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different ...
4
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16 views

How to check for phase separation in polymer simulations?

Suppose I am running a molecular dynamics simulation of a polymer solution that exhibits upper critical solution temperature. From standard solution thermodynamics, we expect to see a polymer-rich ...
5
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80 views

Contribution in action from collisions for a gas?

So if I write the action for a gas: $$ S = \int (T -U) dt $$ where $T$ is the kinetic energy and $U$ is potential energy. I suspect there is a constant term (which does not affect the equations of ...
6
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0answers
47 views

LAMMPS fix print function

First of all, I'm very new to LAMMPS so I'm sorry if my question is trivial. I'm trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-...
8
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1answer
92 views

How to assign "Trajectory Smoothing Window Size" inside VMD Tcl script

Currently in my VMD display, I define the Trajectory Smoothing Window Size in the dialog box as below. Figure below is for protein selection, the Trajectory ...
9
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2answers
242 views

How to simulate peptide solubility using molecular dynamics (GROMACS)?

What's the suggested best practice to simulate peptide solubility? I'm considering to use Gromacs Tutorial Lysozyme in Water as the model. Later, I'm considering to use Radius of Gyration as measure ...
9
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2answers
237 views

How to perform "gmx make_ndx" with single command line bypassing the interactive shell?

Upon creating the index file with gmx make_ndx, we are usually prompted with interactive shell. For example: ...
10
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2answers
254 views

How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

I was performing MD simulation for protein-ligand complex following GROMACS tutorial. I compared the energy of two ligands (S1 and S2) to a protein, using GROMACS LJ-SR (Lennard-Jones Short Range) ...
5
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1answer
59 views

Why are ligands restrained when simulating a protein-ligand complex with MD?

Currently I'm doing an MD simulation of a protein-ligand complex using GROMACS. In the tutorial it mentioned the process of Restraining the Ligand. Why do we do it? Is it absolutely necessary?
8
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1answer
102 views

How to manage disk space for Gromacs XTC (trajectory) file output

I'm running and MD run with this command: gmx mdrun -v -deffnm md It also produces trajectory file with .xtc extension. ...
8
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1answer
70 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 ...
10
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2answers
298 views

Molecular dynamics frame distorted by VMD?

I am running a VMD renderer to view my GROMACS molecular dynamics output. At one frame, the geometry looks fairly normal like this: At another frame, it displays a distorted geometry, with the ...
6
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1answer
132 views

How to visualize protein-ligand complex MD run using VMD

GROMACS version: gmx, version 2021.4 GROMACS modification: No I'm following the Protein-Ligand Complex tutorial. I'd like to visualize the binding using VMD. I use the output from these commands: <...
7
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0answers
39 views

How to determine minimum reasonable MD timing for ligand-protein complex

I am working on protein-ligand complex MD simulation using GROMACS. Now I'm running the tutorial. ...
10
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2answers
98 views

ASE convesion of Trajectory file to XDATCAR

The issue here is while converting a TRAJ file to POSCAR, it works. But, for TRAJ to XDATCAR, it shows TypeError: images should be a sequence of Atoms objects. (...
5
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0answers
38 views

Simple code for polarizable force-field molecular dynamics?

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 ...
13
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2answers
391 views

What kind of systems do we need to coarse-grain to observe interesting phenomena?

When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
8
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1answer
86 views

Use of higher-order integrators in molecular dynamics?

The usual verlet integration scheme for propagating molecular dynamics according to Newton's equations of motion looks like the following: $$ x(t+\Delta t)=2x(t)-x(t-\Delta t)+a(t)\Delta t^2 $$ This ...
6
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1answer
43 views

How do I setup my MSTIS simulation correctly?

I'm trying to setup a Multi State Transition Interface Sampling (MSTIS) simulation to study the ligand binding of my enzyme using OPS and GROMACS. My enzyme acts on small sugar chains and I would like ...
5
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0answers
72 views

How to get the coordination number from RDF in python ovito?

Basically, I am trying to get the running coordination number (CN), but the result isn't correct? I am multiplying the Radial Distribution Function (RDF) with ...
8
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1answer
67 views

What is autocorrelation time?

I'm writing this code of molecular dynamics about a pseudo-ideal gas in a box. The task is integrating the EOM for every atoms for a time-step dt fixed with the leapfrog method and measure the total ...
7
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0answers
76 views

Normalizing the radial distribution function [closed]

The radial distribution function is defined as: $$g(r)=\frac{dn}{4\pi r^{2} dr \rho}.\tag{1}$$ Why, in the calculation, do you divide twice by the number of molecules? What I mean is something like ...
10
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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.
12
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2answers
198 views

Phase transition in Molecular Dynamics simulations

I am reading the book Computer Simulation of Liquids[1] where on multiple occasions it says MD is valid as long as the conditions simulated are away from phase transition. For example, at the ...
9
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2answers
708 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 ...
6
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2answers
149 views

How to initiate protein-ligand docking with MD simulation tools

I have two PDB files (each corresponding to a ligand and a receptor). Each downloaded separately from PDB. I'd like to perform ligand to protein docking process with MD with GROMACS or Amber. Using ...
17
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3answers
2k views

What does ns/day mean in high-performance computing?

In MD simulation benchmarking, you often see performance expressed in terms of ns/day and hours/ns. How do I translate these ...
11
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2answers
506 views

Why can MD simulations not handle "exotic" materials?

We are all aware of the fact that MD Simulations using force fields can treat very big systems. But they cannot handle "exotic" materials. Why?
8
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1answer
69 views

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 ...
29
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2answers
4k views

Can a highly-cited published paper have this type of error?

Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently? Here is my problem: I have been testing a force field published ...
14
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2answers
409 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 ...
7
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1answer
59 views

How Do you Produce your own MEAM Potentials?

I have come across the MEAM Parameter Calibration toolkit (link leads to Wiki, video tutorials, and download link for the package) for fitting your own MEAM potentials [1]. Is this the best software ...
7
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1answer
78 views

Viscosity calculation using molecular dynamics simulations

I use the GROMACS software for MD simulations and I am trying to understand the calculation of viscosity using combinations of different ensembles and different methods. For a non-equilibrium MD ...
12
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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 ...
5
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0answers
65 views

What is the qualitative meaning of the Nosé thermostat?

The Nosé thermostat is explained in Chapter 6 of Understanding Molecular Simulation. Perhaps it's because I find it difficult to follow the derivation, but the physical meaning behind the $s$ ...
11
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1answer
154 views

How would one find a material's equilibrium structure at any specific temperature?

Let's take an example of a simple FCC material, a binary alloy. Above absolute zero K, the alloy will start to disorder and become an FCC solid solution. The alloy would develop defects as it ...
7
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1answer
57 views

Very slow performance for an OPLS-AA methanol simulation

I am running a methanol simulation with a topology I obtained from Tinker for OPLS-AA, at 298 K and 1 bar. This is my .itp file: ...
5
votes
3answers
175 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 ...
11
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3answers
206 views

Quantum chemistry in external electrostatic field?

Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) ...
8
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1answer
169 views

Calculating compressibility from a molecular dynamics simulation: what is meant by "volume fluctuation"?

I am trying to calculate isothermal compressibility from an NPT molecular dynamics simulation, but am not that experienced and don't know how to use an expression from a paper to do it. The part that ...
6
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1answer
83 views

How to fix "bad timestep" error in LAMMPS?

I'm working on this project where I have to simulate a gold nanoparticle impact in a gold plate, my script is: ...
6
votes
1answer
68 views

Radial distribution function for trajectories or time frame?

In many scripts I came across, I saw for the calculation of the RDF, both the trajectory and the individual timeframe also have been used. Can anybody help me with understanding how they are different ...
6
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0answers
76 views

How do you Select a Time Step for Molecular Dynamics Simulations?

It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
7
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0answers
72 views

What's the pair correlation function? What information does it contain?

This question is related to this VASP tutorial, in which the pair correlation function (or radial distribution function: RDF) is utilized to justify whether the solid silicon is melt by AIMD (ab-...
5
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0answers
67 views

Apparent conservation of potential energy in NPT simulation?

I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
7
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2answers
220 views

What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?

I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization. This is the way I understand it: The ...
5
votes
1answer
126 views

What is the equilibrium bond length for a Lennard-Jones potential?

If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
6
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0answers
50 views

How to analyse structure factors calculated from a mixture of isotropic amorphous substrates

I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...

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