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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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)
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
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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How to calculate diffusion coefficient from MSD graph using GROMACS?
In GROMACS I have used the command below to calculate mean square displacement (MSD) over time,
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Radius of gyration and aggregates [closed]
I have performed a MD simulation using GROMACS for a system of 100 caffeine molecules in water. It is expected caffeine form aggregates.
I have calculated the radius of gyration for the simulation ...
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Domain decomposition error while applying bonded restraints - GROMACS
GROMACS version:version 2021.3-MODIFIED
GROMACS modification: Yes
Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
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Is the energy due to external electric field included in gromacs energy?
I have a Gromacs NVT simulation with a constant external electric field using the option "electric-field-z = 1.5 0 0 0".
When calling gmx energy -f (...).edr to calculate the potential ...
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How to add molecules to a specific location in periodic box using gromacs?
In gromacs using the commands, command_1
gmx insert-molecules -f run03.pdb -ci CL.pdb -o out.pdb -nmol 119
will distribute CL ions in the system randomly, but how ...
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Young's modulus from MD simulation [closed]
I have a coarse-grained model of a surface which is almost planar/flat in 2D. Now, I want to compute some of its mechanical properties to test it. Young's modulus is one of the properties that come to ...
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Contact Angle (water droplet on a surface)
I have built a CG model of a surface on which I want to place a water droplet (some water molecules), and calculate the contact angle. Has anyone done similar work with gromacs (MD simulation)? First, ...
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Units of SASA generated from GROMACS gmx_sasa?
I'm wanting to use gmx sasa. I've done this on some residues I'm interested in analyzing. When I look at the output, I expect some value of $\pu{nm^2}$ or maybe $\pu{\unicode[.8,0]{x212B}^2}$. Instead,...
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Gromacs generate forces using .pdb topol.top and .mdp file [closed]
Given the start configuration (.pdb), topology file (topol.top) and run file(water.mdp).
I want to generate the forces on atoms. I tried, using:
...
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How to calculate and plot the electrostatic forces in a .pdb file [closed]
Given a pdb file that looks like the following:
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How to generate a .tpr file from a .pdb or .xyz file in gromacs
I have a .pdb file for a single frame of water in a box. I need to calculate and analyse the electrostatic field for choosing a viable atom in this particular ...
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What does the slope in the viscosity vs shear acceleration graph from non-equilibrium MD signify?
In finding out the viscosity of a system with non-equilibrium MD using GROMACS, an acceleration is given to the system due to which, the velocity profile changes. This change in energy is used to ...
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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 ...
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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:
...
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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) ...
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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?
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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.
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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
...
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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 ...
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