20
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What does "force field" mean?
What is a force field?
The Wikipedia entry on this is a good resource, but I'll give my own description below.
In the context of molecular dynamics (MD), a force field is one way of describing the ...
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12
votes
What does "force field" mean?
The term's origin goes back to vector field which is a function that returns a vector for any given point in space (as in the image below on the left). We can almost "see" that such fields ...
12
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How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?
Which is more appropriate for the binding energy? Neither.
Obi-Wan voice: "These are not the energies you're looking for."
If I understand your goal, you're trying to compare two ligands and ...
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12
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Contact Angle (water droplet on a surface)
For generating the droplet, there are two ways. The 'dumb but it works' way is to just generate a box of water adjacent to the surface, and let it equilibrate in vacuum for a time. The box will ...
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11
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How to simulate peptide solubility using molecular dynamics (GROMACS)?
I'm not sure why you would use radius for gyration as a measure of solubility. Radius of gyration roughly measures how "unfolded" (or more accurately, how "stretched out") a ...
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10
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How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?
I am not a GROMACS user, but have used it once or twice during my course. As far as I can remember and understand, it is common to use different force field in MD if one simulate something solvated in ...
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10
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How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?
Since you seem to have at least a start on automating the process of modifying the file, I will just address the other two parts of your question: the format of the ...
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10
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Molecular dynamics frame distorted by VMD?
Don't Worry, it is not a problem, This happened because you used PBC (Periodic boundary condition) and VMD sometimes has bugs during the visualization in this case. The most important to you to see ...
- 1,652
9
votes
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How to address the errors on Automated Topology Builder?
Did you want to draw Si instead of S? Sulfur atoms bonded to two oxygens and two carbons, like the ones you have drawn here, are at least very rare, if not non-existent. It makes much better sense if ...
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9
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Large pressure fluctuations in molecular dynamics
Large pressure fluctuations are normal for nanoscale simulations of aqueous solutions (and other condensed systems without a gas phase).
Pressure fluctuations are usually enormous in simulations of ...
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9
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Analyzing MD trajectory: molecule orientation
So, with a lot of tries and errors I've found out how to perform such analysis. I'm using a library for Python called MDAnalysis. It can load Gromacs topologies and extract charges from them. Using ...
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9
votes
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How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?
Here's an approach calculating it by hand with numpy. The coordinates are loaded from the trajectory using mdtraj in python:
<...
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9
votes
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Confused about the application/definition of improper torsions
The key thing to remember is that while a "proper" torsion includes atoms 1-2-3-4 with bonds between 1-2, then 2-3, and then 3-4, an improper torsion is just defined by any set of 4 atoms.
...
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9
votes
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How to manage disk space for Gromacs XTC (trajectory) file output
Is there an option in gmx mdrun to specify where to write the .xtc file? For example I want to specify specific directory path ...
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8
votes
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How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?
Short answer
I am a regular GROMACS user. I do not think you can just easily have the total functional form "printed out" from GROMACS. However, you can obtain it from the topology file (...
8
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Does anyone know any software for MD simulation which include the effect of magnetic field?
There is certainly Lammps, which has a fix efield that allows you to apply electric field in your chosen cartesian direction. But I am not sure if it works for your purposes. You can play around with ...
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8
votes
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How can I decide on the order of different monomers in a co-polymer?
This is a question that cannot have a "right" answer. As mentioned in the comments, the answer would depend on the experimental system and on the specific properties you want to reproduce.
...
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8
votes
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Finding parameters for a molecule in various forcefields
Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do:
...
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8
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What does "force field" mean?
Molecular dynamics is based in Molecular Mechanics. Molecular Mechanics do many approximations in order to treat the atomic/molecular system. A good definition can be seen here:
Molecular Mechanics ...
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8
votes
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What does the slope in the viscosity vs shear acceleration graph from non-equilibrium MD signify?
This is shear thinning.
This kind of non-Newtonian behaviour is not really important for simple fluids like water at macroscopic scales, but it is readily observable in simulations of small systems on ...
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7
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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 believe I have figured it out.
For those trying to martinize their all-atom files into coarse grain representations for martini 3, use the following package:
https://github.com/marrink-lab/vermouth-...
- 423
7
votes
Error in GROMACS for adding ions to a solution
As I had previously written in the comments, the warning given by gromacs seems to indicate that the GROMOS force fields should not be used due to wrong parameterization:
...
- 7,171
7
votes
How to initiate protein-ligand docking with MD simulation tools
You can do it either way.
You need to give predocked files to GROMACS/Amber for running protein-ligand complex molecular simulations. Also have a look at HADDOCK web server for predocking.
Place the ...
- 1,461
7
votes
Confused about the application/definition of improper torsions
A plane can be defined with 3 atoms and two planes can be defined with 4 atoms. Thus it's natural to define an angle between these two planes which is the dihedral (or torsion) angle.
You can think of ...
- 171
7
votes
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How to visualize protein-ligand complex MD run using VMD
First, You need to click on Create Rep and you will get a new line in the box below as the picture attached (with the same name "protein" in your case).
To show the ligand, you should know ...
- 1,652
7
votes
Alternative to CGenFF for generating large ligand topology
I'd use OpenMM's openmmforcefields package, which is available on GitHub.
I haven't used it extensively, but I recommended to a student in a colleague's lab and ...
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7
votes
Accepted
How to perform "gmx make_ndx" with single command line bypassing the interactive shell?
Note: there's nothing specific to Gromacs in the answer below. These are just shell scripting techniques that are relevant to any program that takes input from stdin...
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7
votes
How to perform "gmx make_ndx" with single command line bypassing the interactive shell?
How about this, also writes to a log file. This selects both group 1 and group 13 and write the indices to a index file (index.ndx)
...
- 1,461
7
votes
How to simulate peptide solubility using molecular dynamics (GROMACS)?
You need the chemical potential to do solubility
The problem with solubility of large molecules, is that you need to know the chemical potential in the liquid and the solid. You can use Free Energy ...
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7
votes
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How to generate a .tpr file from a .pdb or .xyz file in gromacs
For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp).
Assuming, you are working with amber forcefield (a99ffSBdisp), Here's how I ...
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