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.
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What is the simplest classical force field to set up?
What is the simplest force field to set up?
I need to generate the potential energy of some conformers of amino acids and ligands in xyz files. I am not too concerned about the force field other than ...
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How to decouple the Lennard-Jones (LJ) interaction between two particular atoms in a same molecule?
I would like to decouple the lennard-jones (LJ) interaction between two atoms of the same molecule. These atoms obviously doesn't have any bonded interactions between them, so only the non-bonded ...
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martinize issue
PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb
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Fix the distance restraint between two set of molecules in gromacs
it seems that in GROMACS we can apply distance restraint between two atoms/particles. However, does anyone know if one can apply a distance restraint between whole two set of molecules, like apply a ...
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Relation between force constant of the bonded parameters, time constant and the dynamics of the system
I want to understand these things in both intuitive and non-intuitive ways. In some cases, we constrain hydrogens so that we can run molecular dynamics at a higher time step than we normally would, ...
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Check for steric clashes before doing minimization
Are there already some tools available, or we can code for finding the atoms/residues that can contribute the steric clashes before minimization solve the issue?
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GROMACS gmx energy LJ (SR) Calculation
I am looking at simple MD simulations of homogeneous Lennard-Jones (LJ) liquids to understand GROMACS’s parameters before moving onto more complex systems.
Currently, I am having an issue replicating ...
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Does GROMACS have the capability to do Monte Carlo simulation of proteins?
My supervisor says that GROMACS can do both (all-atom) MD and MC simulations of proteins.
I never found anything while searching the Internet about MC-only simulations. As far as I found, GROMACS can ...
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Restrain a protein to be helical in an MD simulation
I have a very small part of a protein that is supposed to be helical. However, in molecular dynamics simulation, it unfolds and gets into extended conformation. Is there any way I can force it to stay ...
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Given a .gro file of a monomer, how to polymerize it?
I have a structure (.gro) file of a PolyEthylene Glycol (PEG) molecule as shown below. How do I get the corresponding structure file for PEG-20 i.e., a molecule with a degree of polymerization=20, ...
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Velocity autocorrelation function for molecular dynamics trajectory
I have a 1 ns long molecular dynamics trajectory of 884 molecules of water, and I am trying to compute the velocity autocorrelation function using MDAnalysis to analyze the GROMACS output files.
I ...
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How to compute the Elastic Modulus of a molecule using GROMACS?
Say we take the basic example of a PEG molecule (PolyEthylene Glycol). What is the fundamental physics for computing the Elastic Modulus or the Young's Modulus from the Molecular Dynamics (MD) ...
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Error with running GROMACS with SLURM [closed]
I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows:
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Eliminate the entropic contribution in the free energy of dimerization between two molecules in umbrella sampling
For my set-up to compute the free energy of dimerization between two molecules in a solvent using umbrella sampling, I can see that there is an entropic contribution since I have used distance as a ...
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How to convert a SMILES into a LAMMPS or GROMACS input file?
Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)?
Demonstrate ...
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Compute the monomeric fraction in MD simulation
I have a system of molecules in two different solvents in which aggregation occurs, but visually in different ways. In one, aggregation occurs rapidly, but in another sparsely. These MD simulations ...
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gromacs: How to keep only the last group in the NDX file created using make_ndx?
Using the following Gromacs utility execited from Bash, I can create a new group in the ndx file:
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Is water penetration and fatty acid dissolution reasonable when Gromacs modelling of an aqueous lipid bilayer?
as mentioned, I'm building a molecular dynamics simulation of decanoic acid and decanoate (with neutralising sodium cations) in water. I've minimized and equilibrated the simulation up to 295 K and I'...
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How do we calculate diffusion coefficient when GROMACS MSD graph with two slopes?
I calculated the MSD using the gmx msd -f run05.part0005.xtc -s run05.tpr -o msd_200-250ns.xvg. As a result, I got a graph with 2 slopes as attached.
In the MD simulation, I followed a simulated ...
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Lattice constant of an FCC crystal from molecular dynamics simulation
So, I have a system of n number of molecules inside a box which is supposed to be solid. I performed the md simulation of the system using stochastic integrator in a box. I know the lattice of the ...
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Is there a way to force GROMACS to keep a certain density for water?
I am trying to fully populate my GROMACS simulation, but the water density in the bulk is too low.
Here are the steps I used:
Add organic monolayer into 9x9x9 box
Solvate with water
equilibrate t-...
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CHARMM36 Parameters for Neutral Arginine
I am looking for CHARMM36 parameters for Neutral Arginine. Protonated form of Argnine is already available in CHARMM36 library, but not the same for Neutral. Thanks.
With best regards
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Adsorption of naphthalene on graphene oxide sheets with gmx
How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?
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How to automate GROMACS analysis in a bash script?
I am trying to write the analysis using gmx energy in a bash script. When this is usually passed on a command line, it asks for an input from keyboard to choose the energy term from a list of terms.
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How is the equation for the position of a virtual site derived?
Cross posted on Math SE
I am trying to understand virtual sites in MD simulations, and I came across this configuration:
Here, coordinate $\mathbf{s}$ represents the virtual site, which is formed by ...
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MMGBSA: Electrostatic and van der Waals
I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
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Quantifying binding free energy?
I have binding free energy of some organic molecules on a surface, computed through Umbrella sampling. For now, I only have experimental data on the binding energy of some of these molecules. Is it ...
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Error Simulating bulk diemthyl-ether with angle constrain in gromacs
I am trying to simulate bulk dimethyl ether with total constraints, both bonds and angles.
I am using lincs with constraint = all-angles in *.mdp file in gromacs.
I am attaching the error I ...
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Establishing AAs protonation - which software to choose?
I need to establish protonation of aminoacids composing the studied protein. To my knowledge there are H++ and Pdb2pqr servers that are able to do that. However, they yield quite much different ...
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Keeping a coarse grained particle off plane (Molecular Dynamics)
I have a coarse-grained particle (bead) that I want to keep off the plane from the plane of other beads which form like a 2D plane. Do people employ improper dihedral for this or any other bonded ...
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Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment) [closed]
I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
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Looking for the OPLS parameters for octanol
I have been looking for OPLS gromacs parameters for 1-octanol, but haven't been able to get it. Doing a quick web search takes me into links for lipidbook, from which I can't download at all from ...
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Time evolution of angle made by the helix with the normal to the plane using gromacs
I am new to the md simulation community. I have a peptide which is helical in a bilayer. I want to calculate the angle of the peptide relative to the bilayer with gromacs. For that, I created an index ...
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Gromacs simulation with 100 copies of same ligand appears weird [closed]
I'm a gromacs noob, so I appreciate your patience. I tried simulating the interaction of a protein with 100 copies of the same ligand, in water. The workflow I used is attached here as a picture. The ...
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DFT calculations [duplicate]
What is the best way to learn DFT (Density Functional Theory) for beginners?
I want to learn DFT (both simulation and theory). I am a beginners in this field. What is the best way to learn it?
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How do I get openMPI to run with gromacs? [closed]
When I run the command
mpirun -np 48 mdrun_mpi -deffnm md -v, the software works with no error, but it only runs as fast as when I'm using 1 CPU (the computer I'm ...
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Contribution to pressure tensor from water
Cross-posted later on Reddit.
I have an infinite CG model of the material solvated in water. I am trying to apply a uniaxial deformation along a particular x-axis; the mdp settings in GROMACS are ...
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Model coordination complex using GROMACS or CP2K
Is it possible to compute a 3D model of a calcium EDTA complex and it's energy? If so, how should I go about doing it or where can I obtain relevant information regarding computation methods?
I ...
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Difference between two pull codes in gromacs (SMD)
My molecule is aligned along x-axis, and I want to pull this molecule along x-axis with one end defined as the first pull group, and another end as the second pull group. I have two pull codes, which ...
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Thermal conductivity in GROMACS? [closed]
Is there any way we can calculate thermal conductivity in GROMACS? I can see the equilibrium Green-Kubo method algorithm, or non-equilibrium Muller-Plathe algorithm implemented in LAMMPS, but don't ...
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Bending rigidity of the nanomaterial from MD simulation
The literature seems to be very diverse in measuring the bending rigidity of the nanomaterial from MD simulation. I have seen people often use this relation from continuum mechanics $$k = \frac{Eh^3}{...
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Perform energy minimization of multiple models of protein-dna complexes
Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)?
I know of GROMACS or Chimera or the online servers but is ...
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How to control the thickness of lipid bilayer with GROMACS
I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial.
I can successfully orient the protein in the lipid (turquoise) as you can see in the image below:
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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 ...
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Density of a spherical droplet of water on top of graphene
I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
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How to compute 2D density maps in GROMACS?
I have a GROMACS trajectory of MD simulation. I want to make a contour plot of density as a function of two coordinates, namely X and Z. Is it possible to get this using ...
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Three point bending test on a 2D nanomaterial with SMD in gromacs
I want to see the bending response of my 2D nanomaterial, where the force is applied at the midpoint of the sheet using SMD (constant-velocity). Here, I have kept the two ends fixed. So, I want to ...
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Martini 3 CG water cluster is not becoming spherical under NVT conditions [closed]
When we put a certain number of molecules in a small cubic box, and put it inside a large cubic box, under NVT simulation, the water cubic box is supposed to be spherical in shape to reach a minimum ...
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Stress on pulling in MD simulation [closed]
In gromacs, if we use SMD to pull one end of the molecule, how can we compute the stress applied if we know the force. I am using plumed to define a colvar, and pulling one end of my molecule. Thanks.
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Calculating bending modulus of a CG model of a surface from MD simulation [closed]
I have built a CG (Martini) model of a 2D Nanomaterial. For now, I want to calculate its bending rigidity. As far as I know, the bending modulus can be computed by making the nanomaterial infinite - i....
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