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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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 ...
Bruce Zhou's user avatar
4 votes
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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 ...
Roshan Shrestha's user avatar
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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 ...
anupama's user avatar
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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 ...
farmaceut's user avatar
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7 votes
1 answer
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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 ...
Roshan Shrestha's user avatar
4 votes
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61 views

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 ...
Saha_1994's user avatar
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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 ...
Roshan Shrestha's user avatar
4 votes
1 answer
95 views

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 ...
Anna VDP's user avatar
2 votes
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88 views

Gromacs simulation with 100 copies of same ligand appears weird

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 ...
hbc8's user avatar
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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?
Tom's user avatar
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How do I get openMPI to run with gromacs?

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 ...
hbc8's user avatar
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4 votes
1 answer
193 views

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 ...
Roshan Shrestha's user avatar
3 votes
1 answer
91 views

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 ...
beardeadclown's user avatar
3 votes
1 answer
333 views

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 ...
Roshan Shrestha's user avatar
3 votes
0 answers
84 views

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 ...
Roshan Shrestha's user avatar
3 votes
1 answer
55 views

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}{...
Roshan Shrestha's user avatar
3 votes
1 answer
50 views

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 ...
Lily Sharpton's user avatar
2 votes
1 answer
120 views

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: ...
littleworth's user avatar
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3 votes
2 answers
310 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 ...
littleworth's user avatar
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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 ...
Roshan Shrestha's user avatar
3 votes
2 answers
354 views

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 ...
Roshan Shrestha's user avatar
4 votes
0 answers
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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 ...
Roshan Shrestha's user avatar
2 votes
0 answers
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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 ...
Roshan Shrestha's user avatar
3 votes
0 answers
75 views

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.
Roshan Shrestha's user avatar
5 votes
0 answers
88 views

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....
Roshan Shrestha's user avatar
6 votes
2 answers
2k views

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, ...
Night Shade's user avatar
4 votes
0 answers
91 views

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 ...
Ravi's user avatar
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3 votes
1 answer
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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 ...
Vasista's user avatar
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3 votes
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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 ...
curio's user avatar
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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 ...
Night Shade's user avatar
8 votes
0 answers
159 views

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 ...
Roshan Shrestha's user avatar
10 votes
1 answer
330 views

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, ...
Roshan Shrestha's user avatar
3 votes
1 answer
526 views

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,...
German Barcenas's user avatar
4 votes
0 answers
53 views

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: ...
fireball.1's user avatar
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7 votes
1 answer
460 views

Gromacs generate charges for a .pdb file

I have a .pdb file containing water molecules. ...
fireball.1's user avatar
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6 votes
0 answers
108 views

How to calculate and plot the electrostatic forces in a .pdb file [closed]

Given a pdb file that looks like the following: ...
fireball.1's user avatar
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7 votes
1 answer
2k views

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 ...
fireball.1's user avatar
  • 1,083
10 votes
1 answer
111 views

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 ...
Kavya Mrudula's user avatar
9 votes
2 answers
501 views

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 ...
littleworth's user avatar
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10 votes
3 answers
2k views

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: ...
littleworth's user avatar
  • 1,654
11 votes
2 answers
1k views

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) ...
littleworth's user avatar
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5 votes
1 answer
440 views

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?
littleworth's user avatar
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9 votes
1 answer
934 views

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. ...
littleworth's user avatar
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8 votes
1 answer
423 views

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 ...
littleworth's user avatar
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10 votes
2 answers
922 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 ...
littleworth's user avatar
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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: <...
littleworth's user avatar
  • 1,654
7 votes
0 answers
138 views

How to determine minimum reasonable MD timing for ligand-protein complex [closed]

I am working on protein-ligand complex MD simulation using GROMACS. Now I'm running the tutorial. ...
littleworth's user avatar
  • 1,654
8 votes
2 answers
688 views

Confused about the application/definition of improper torsions

The only basic definition of improper torsion/improper dihedral I have is - improper dihedral is formed when we have a central atom bonded to the three atoms. Can anyone help me visualize/help to ...
Roshan Shrestha's user avatar
6 votes
1 answer
78 views

How do I setup my MSTIS simulation correctly?

I'm trying to setup a Multi State Transition Interface Sampling (MSTIS) simulation to study the ligand binding of my enzyme using OPS and GROMACS. My enzyme acts on small sugar chains and I would like ...
Martin Bonin's user avatar
8 votes
0 answers
274 views

How to add double bonds to hexagons when creating a graphene layer in VMD? [closed]

When creating a Graphene layer in VMD using the Nanotube Builder it only generates hexagons with single bonds because of this errors occur when creating the topology for gromacs software using, ...
Night Shade's user avatar