Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
209
questions
3
votes
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
votes
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
votes
0answers
11 views
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
votes
0answers
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
votes
0answers
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
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 ...
5
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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 ...
