How to calculate water volume between interface of 2 proteins using Gromacs?

04 May 2017 5,188 0 View

How to make a movement of Ub-attached-Helix in protein component by MD approach?

Dear gmx user I am Gromacs version 4.6.7 user. I am working on a protein which has Ub (Ubiquitin) binding domain having strong affinity for Ub. On one side, protein has ubiquitin binding domain...

08 September 2016 3,661 7 View

How to calculate "12-6 Lennard-Jones (LJ) Nonbonded" parameter?

07 August 2016 4,631 4 View

How can I resist isopeptide [C- - - NZ] bond through out simulation in Gromacs?

HI I have attached Ubiquitin (Ub) C-term Gly to N-term Lys of a substrate protein via iso-peptide bond [C---NZ] (for ubiquitination) using Pymol and Coot. But when I do energy minimization,...

04 May 2016 4,525 2 View

Any advice on ligand structure alignment against ligand database?

Hi All I have crystal structure of my ligand and I need to know the similar ligand structures from ligand database. Is there any tool/server which performs ligand structural alignment for my...

08 September 2015 3,866 7 View

In Gromacs, how do I fix a problem regarding "Unknown left-hand 'cutoff-scheme' in parameter file"?

Hi I am working on Gromacs 4.5.6 and system contains protein+sol+Ligand. I have to neutralize the system by adding NA and CL but when I use parameter file ions.mdp (attached), the following...

04 May 2015 8,908 7 View

Ligand coordinates are removed after making box [protein ligand complex Molecular dynamics issue]?

Dear Scientists I want to make system for protein ligand complex for simulation study on Gromacs 4.5.6. I follow Justin tutorial...

04 May 2015 4,725 1 View

How can I refine an unusual bond in the protein structure?

I have attached flexible linker to a protein but found some unusual bonds (at attachment point 3-4 extra bonds found in attaching amino acid residue) at the point of attachment, I used coot for...

03 April 2015 735 4 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View