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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19 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 ...
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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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244 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: ...
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261 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) ...
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1answer
60 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?
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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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1answer
72 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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301 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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134 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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42 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. ...
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1answer
49 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 ...
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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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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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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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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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123 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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Calculate FF interaction energy of small molecular dimers

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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79 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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1answer
58 views

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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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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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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1answer
149 views

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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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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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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139 views

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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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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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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1answer
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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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390 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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218 views

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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1answer
372 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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1answer
175 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 ...
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218 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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498 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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1answer
72 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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1answer
553 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 ...
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How to effectively simulate high density systems in GROMACS? [closed]

I have a system with a dense liquid solvent and a polymer solute. I have inserted all the molecules randomly using gmx insert-molecules and then did the energy ...
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1answer
150 views

Is there a way to understand pi-pi interactions through GROMACS?

I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I ...
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1answer
61 views

Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
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1answer
393 views

Why does my calculation using GROMACS get stuck at step 0?

I have been using the HPCE on our campus for MD simulations using GROMACS. However, when I use the following script, after the job starts to run on the cluster, gets stuck at Step 0 in the log file. <...
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158 views

Is it possible to simulate the Raman spectra via Molecular Dynamics (MD) using the GROMACS package?

I'm new to molecular dynamics and DFT. The aim was to study the Raman spectra of a molecule in a medium. As we know the Raman spectra of a molecule change due to the induced polarization in the ...
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158 views

Computational biology textbook similar to "Computational Materials Science" by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD ...
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How to do molecular dynamics calculations and analyse trajectories of small molecules? [closed]

I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is protein cofactor (FAD) small molecule (either single O2 molecule or single Chlorine atom) ...
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161 views

Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?

I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
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1answer
95 views

How can I decide on the order of different monomers in a co-polymer?

While performing molecular dynamics simulations on a co-polymer, how long should the minimum size of the polymer be, to replicate the experimental properties with a reasonable error? Within this ...
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3answers
270 views

Does anyone know any software for MD simulation which include the effect of magnetic field?

I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
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276 views

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

This is a doubt regarding the usage of various forcefields together in MD simulation of hydrates. For Eg., we use TIP4P/ice for water molecules, OPLS-UA for methane and EPM2 for carbon dioxide and so ...