Questions tagged [gromacs]
GROMACS software package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Primarily designed for biochemical molecules like proteins, lipids and nucleic acids.
10
questions
14
votes
2
answers
890
views
Finding parameters for a molecule in various forcefields
Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...
- 4,141
13
votes
3
answers
4k
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.
- 1,674
12
votes
1
answer
2k
views
Compute RDF between COMs of two selections (or groups) using GROMACS
I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
- 493
11
votes
1
answer
318
views
Unable to recreate data for benzene from paper in GROMACS 2020.5
I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
- 4,141
10
votes
2
answers
1k
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 ...
- 1,674
9
votes
2
answers
2k
views
Large pressure fluctuations in molecular dynamics
I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level.
For example, I set the pressure at 1 bar and it averages ...
- 2,363
8
votes
0
answers
123
views
Calculate FF interaction energy of small molecular dimers [closed]
I have a set of molecular dimers (~25 atoms) for which DFT-D3 interaction energies are calculated by Psi4 and Turbomole program. Now I want to compare these values against Force-Field methods like UFF/...
- 810
7
votes
2
answers
184
views
Import an initial trajectory into OPS without OpenMM
I'm trying to use openpathsampling to simulate the binding of a ligand to my enzyme. I'm using Gromacs for my normal simulation on the HPC system provided by my university. I created an initial ...
- 143
6
votes
1
answer
1k
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:
<...
- 1,674
4
votes
2
answers
360
views
How to orient the protein for lipid bilayer simulation in Gromacs
I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer.
The domain of the protein looks like this:
Thus I'd like to have the transmembrane part of the protein to be buried in lipid ...
- 1,674