Questions tagged [molecular-dynamics]
For questions related to the use of or theory behind classical or ab initio molecular dynamics.
401
questions
8
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1
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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 ...
- 1,674
9
votes
2
answers
534
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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 ...
- 1,674
10
votes
3
answers
2k
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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:
...
- 1,674
11
votes
2
answers
1k
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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) ...
- 1,674
5
votes
1
answer
489
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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?
- 1,674
9
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1
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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.
...
- 1,674
8
votes
1
answer
480
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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
...
- 1,674
10
votes
2
answers
1k
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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 ...
- 1,674
6
votes
1
answer
1k
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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:
<...
- 1,674
7
votes
0
answers
147
views
How to determine minimum reasonable MD timing for ligand-protein complex [closed]
I am working on protein-ligand complex MD simulation using GROMACS.
Now I'm running the tutorial.
...
- 1,674
10
votes
2
answers
1k
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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. (...
- 949
6
votes
0
answers
77
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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 ...
- 1,040
12
votes
2
answers
433
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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 ...
- 4,141
8
votes
1
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184
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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 ...
- 3,524
7
votes
1
answer
86
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 ...
- 143
5
votes
0
answers
605
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How to get the coordination number from RDF in python ovito? [closed]
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 ...
- 949
9
votes
1
answer
665
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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 ...
- 91
13
votes
3
answers
4k
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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.
- 1,674
12
votes
2
answers
706
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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 ...
- 255
10
votes
2
answers
3k
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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 ...
- 1,674
6
votes
2
answers
1k
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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 ...
- 1,674
17
votes
3
answers
3k
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 ...
- 1,674
12
votes
2
answers
583
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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?
- 1,481
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1
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95
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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 ...
- 719
30
votes
2
answers
4k
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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 ...
- 809
14
votes
2
answers
709
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 ...
user2026
7
votes
1
answer
186
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 ...
- 929
8
votes
1
answer
725
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 ...
- 1,407
11
votes
1
answer
192
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 ...
- 1,977
5
votes
0
answers
92
views
What is the qualitative meaning of the Nosé thermostat? [closed]
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 $s$ ...
- 929
11
votes
1
answer
243
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 ...
- 5,125
8
votes
1
answer
142
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:
...
- 4,141
6
votes
3
answers
1k
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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 ...
- 81
13
votes
3
answers
465
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) ...
- 801
9
votes
1
answer
549
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 ...
- 719
6
votes
1
answer
273
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:
...
Rodolfo Damián Chapa González
7
votes
1
answer
429
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 ...
- 949
6
votes
0
answers
217
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 ...
- 929
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votes
0
answers
362
views
What's the pair correlation function? What information does it contain? [closed]
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-...
- 14.9k
6
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0
answers
195
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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 ...
- 809
7
votes
2
answers
268
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
1
answer
1k
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. ...
- 564
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0
answers
144
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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 ...
- 2,262
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0
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42
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How do I model drug diffusion from polymeric matrix? [closed]
I have been redirected to this forum from Chemistry SE.
My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
- 51
2
votes
0
answers
52
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Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]
Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
- 81
7
votes
0
answers
66
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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria
My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
- 2,262
10
votes
0
answers
377
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Setup for 4-point flexible water model [closed]
I tried to search online if there are examples or suggestions on how to set up a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc., but there's no clear example ...
- 2,262
13
votes
1
answer
706
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How to calculate RDFs for MD trajectories without PBC, directly from coordinates? [closed]
I have been running MD simulations on water droplets with an ion in them. I am trying to implement a program that could calculate the radial distribution function from ion to oxygen (or ion to ...
- 6,516
12
votes
3
answers
400
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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?
user2026
6
votes
0
answers
584
views
Back-mapping Martini 3 coarse-grain to all-atom representations [closed]
I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements.
I am using MartiniTools for ...
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