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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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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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4 votes
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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. ...
Kavya Mrudula's user avatar
4 votes
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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
4 votes
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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
4 votes
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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
3 votes
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35 views

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 ...
Roshan Shrestha's user avatar
2 votes
0 answers
42 views

Error with running GROMACS with SLURM

I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows: ...
Pranoy Ray's user avatar
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2 votes
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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 ...
Roshan Shrestha's user avatar
2 votes
0 answers
32 views

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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