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16 votes
Accepted

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 ...
  • 1,887
12 votes
Accepted

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 ...
  • 1,887
11 votes
Accepted

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 ...
  • 778
11 votes

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 ...
  • 1,887
10 votes

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 ...
8 votes
Accepted

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 ...
  • 5,834
8 votes
Accepted

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 ...
  • 331
8 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 ...
  • 29.1k
7 votes
Accepted

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 ...
  • 974
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 ...
  • 4,066
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) ...
  • 974
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...
  • 1,887
7 votes
Accepted

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 ...
7 votes
Accepted

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. ...
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 ...
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 ...
  • 974
7 votes

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 ...
  • 19.3k
6 votes

How to initiate protein-ligand docking with MD simulation tools

Docking and Molecular dynamics are two very different process. In docking, you will need the ligand (normally in a separate file), the protein (can be in a separate file too), and the information ...
  • 19.3k
6 votes
Accepted

Import an initial trajectory into OPS without OpenMM

Snapshot types in OpenPathSampling depend on the type of engine you're using. To some extent, snapshot types can be interchanged (if you had OpenMM available, I think the approach you're trying would ...
  • 1,887
5 votes

Import an initial trajectory into OPS without OpenMM

Note: not surprisingly, this answer doesn't resolve the main issue. See dwhswenson's answer for a full fix. ...
  • 14.3k
5 votes

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

Just complementing the @dwhswenson answer, when studying ligand/protein binding process, there is no best energy to look for. In the binding process there are several mechanism that will influence it. ...
  • 19.3k
5 votes
Accepted

Units of SASA generated from GROMACS gmx_sasa?

The unit is actually $\pu{nm^2}$. What is written there is not is not specific to GROMACS, but to the plotting program it is using Xmgrace. \S denotes the start of ...
4 votes

Gromacs generate charges for a .pdb file

GROMACS keeps internal topology files for common water models. You are clearly using a 3-point water model such as spc, spc/e, tip3p, OPC3 etc. You can also supply your own topology file. Here is a ...
  • 1,030
4 votes
Accepted

Very slow performance for an OPLS-AA methanol simulation

After running some tests, the best way to overcome the slow performance was to simply use the constraints no h-bonds. There was no significant difference in ...
  • 3,947
4 votes

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

The cause to use restrains is due to a previous knowledge (i.e. experimental) of system behavior/characteristics that you want to include/retain/reproduce in your simulations. In the case of protein-...
  • 19.3k
4 votes
Accepted

Molecular dynamics frame distorted by VMD?

Its neither a biophysical effect nor a bug in your MD simulation steps. It's just an visualisation issue. You could use the gmx trjconv command to make your protein ...
  • 974
3 votes

How do I setup my MSTIS simulation correctly?

This is a great question, with a lot to unpack in it. (In other words, strap in for a long answer.) There's a bit of an XY problem here: the specific question asked is a good one, but I think the more ...
  • 1,887
3 votes
Accepted

How to calculate diffusion coefficient from MSD graph using GROMACS?

MSD accuracy decreases as a function of the lag-time $t$, because for large $t$ there are fewer pairs of time slices of interval $t$ to average over. Think of the limit in calculating MSD for the ...
  • 613
3 votes

How to calculate diffusion coefficient from MSD graph using GROMACS?

If you can obtain the raw data used in that plot, as a purely statistical and numerical exercise you can determine the interval which will give you minimum uncertainty in the estimate of the gradient. ...
3 votes

How to orient the protein for lipid bilayer simulation in Gromacs

In the Step One: Prepare the Topology, second paragraph, you can find the following information: The peptide was prepared in-house using the xLeap module of AmberTools, using ideal backbone geometry ...
  • 19.3k

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