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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Martini 3 CG water cluster is not becoming spherical under NVT conditions

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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3 votes
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Stress on pulling in MD simulation

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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5 votes
2 answers
201 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, ...
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33 views

Radius of gyration and aggregates

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 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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6 votes
1 answer
212 views

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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8 votes
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Young's modulus from MD simulation

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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10 votes
1 answer
112 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, ...
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3 votes
1 answer
141 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,...
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4 votes
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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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7 votes
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Gromacs generate charges for a .pdb file

I have a .pdb file containing water molecules. ...
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6 votes
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How to calculate and plot the electrostatic forces in a .pdb file

Given a pdb file that looks like the following: ...
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7 votes
1 answer
431 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 ...
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10 votes
1 answer
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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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9 votes
2 answers
311 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 ...
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10 votes
3 answers
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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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11 votes
2 answers
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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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  • 1,542
5 votes
1 answer
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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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8 votes
1 answer
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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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8 votes
1 answer
188 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 ...
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10 votes
2 answers
388 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 ...
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6 votes
1 answer
324 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: <...
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7 votes
0 answers
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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. ...
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  • 1,542
8 votes
1 answer
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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 ...
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6 votes
1 answer
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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 ...
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8 votes
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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, ...
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11 votes
3 answers
3k 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.
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6 votes
2 answers
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How to initiate protein-ligand docking with MD simulation tools

I have two PDB files (each corresponding to a ligand and a receptor). Each downloaded separately from PDB. I'd like to perform ligand to protein docking process with MD with GROMACS or Amber. Using ...
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7 votes
2 answers
140 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 ...
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8 votes
0 answers
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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/...
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7 votes
1 answer
243 views

Viscosity calculation using molecular dynamics simulations

I use the GROMACS software for MD simulations and I am trying to understand the calculation of viscosity using combinations of different ensembles and different methods. For a non-equilibrium MD ...
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8 votes
1 answer
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Very slow performance for an OPLS-AA methanol simulation

I am running a methanol simulation with a topology I obtained from Tinker for OPLS-AA, at 298 K and 1 bar. This is my .itp file: ...
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10 votes
0 answers
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Setup for 4-point flexible water model [closed]

I tried to search online if there are examples or suggestions on how to set up a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc., but there's no clear example ...
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6 votes
0 answers
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Back-mapping Martini 3 coarse-grain to all-atom representations [closed]

I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements. I am using MartiniTools for ...
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9 votes
1 answer
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What is the purpose of DSSP when using martinize2?

I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...
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10 votes
2 answers
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How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
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10 votes
1 answer
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What does vacuum signify in the simulation box after the simulation?

While carrying out constant volume simulations, I've observed that sometimes when the gaseous molecules come closer from their initial spacing, an empty space is created in the box. As I should ...
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8 votes
1 answer
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How to address the errors on Automated Topology Builder?

I was trying to get the charges and the topology file for this molecule ($\ce{C28H58O7S8}$). But I get the following error despite using the right number of hydrogens. ...
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8 votes
0 answers
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How to go from tinker parameters to a GROMACS itp file, specifically for dihedrals? [closed]

I am trying to write an itp file for the compound 1,2-diethoxyethance (CCOCCOCC).I used tinker analyze to obtain the parameter file, f2.out, which I have attached to this post. In order to check if my ...
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7 votes
1 answer
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How to go from Tinker parameter file to GROMACS topology file for improper and proper dihedrals?

I have been playing with a polymer called glyme, and I have run Tinker analyze on it to get OPLS-AA parameters for it. I have attached the output parameter file to this post. My question is, how do I ...
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3 votes
1 answer
100 views

Missing residues in ATB downloaded pdb/rtp files

I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md) Two files are available: a PDB file and a topology ITP/RTP file. The name of the ...
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9 votes
2 answers
779 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 ...
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12 votes
1 answer
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Analyzing MD trajectory: molecule orientation

I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field. There are two order parameters that are used to ...
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10 votes
1 answer
638 views

How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?

I am simulating a droplet of water with GROMACS. The droplet consists of about 200 TIP3P water molecules and is placed near the center of a large, mostly empty box (...
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11 votes
1 answer
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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 ...
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14 votes
2 answers
338 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 ...
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6 votes
1 answer
855 views

Error in GROMACS for adding ions to a solution

I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS. I believe I have followed the process to the T. I would like to mention that in the "Generate Topology&...
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5 votes
1 answer
107 views

How to overcome gromacs make_ndx automatic ranking of atomic indexes?

When working with gmx make_ndx I found very annoying the fact that atomic indexes are automatically ranked in the outputted index ...
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