I would like to know how do i set up the parameters related to the external electromagnetic fields in my mdp file?

Gromacs, molecular dynamic simulation

08 September 2016 8,819 0 View

How can i use gromacs g-files to extract the z-coordinates of all the ions of gromacs output?

gromac, md,

06 July 2015 1,194 0 View

Is it possible to compute ion conductivity using existing Gromacs tools? How might I calculate ionic conductance through bilayer in gromacs?

ionic current, gromacs

04 May 2015 3,429 1 View

When I run the trjconv ,who to select the two group together for the output?

gromacs

03 April 2015 4,047 1 View

How should I set up the parameters of the external electric field in mdp file?

Application of electric fields in molecular dynamic simulation (GROMACS).

01 February 2015 8,096 7 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

Which is the most efficient etching solution for nickel based alloys?

Which solution reveals the microstructure and features of nickel-based alloys?

02 March 2021 2,221 3 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

Which reagent is best among 'Dimethylglyoxime" and "Dithiothreitol" for spectroscopic determination of Nickel ?

What I think is Dithiothreitol. As it is water-soluble and does not form a precipitate. But, the thing is it contains sulphur which is quite hazardous to aquatic animals.

01 March 2021 8,374 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