How do I calculate ionic current with Gromacs?

10 November 2015 874 8 View

How can I change OPLS/AA force field parameter to CHARMM force field?

07 August 2015 8,834 11 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

How to quantify carbon deposition on CuZnAl catalyst?

Dear All, I want to quantify carbon deposition on the surface of the CuZnAl catalyst. I have tried thermogravimetric analysis, but I've got weight gain as the active Cu- get oxidised. Does anyone...

01 March 2021 1,907 3 View

Why Trivalent chromium start precipitating above PH 5 ? Moreover discuss difference between adsorption of chromium and precipitation of chromium ?

I am a student of MS Environmental Engineering and started my research phase. I am working on metal removal ( chromium iii ) by using activated carbon prepared from the agricultural feedstock. So...

01 March 2021 5,475 2 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

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

Can anyone share his experience regards Smoothing in origin?

I am working on TiO2 composite material and the results of XRD have a lot of small/junk peaks and while I apply a smooth filter in Origin then the other characteristics peaks disappear so anyone...

26 February 2021 8,183 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

CGA 300 Regulator for CO2 cylinder?

Has anyone ever tried to deliver CO2 with a CGA 300 regulator? I know that a CGA 320 regulator is standard for CO2. The issue is that I currently do not have any free CGA 320 regulators. I also...

25 February 2021 3,292 3 View

What are the methods used for CNT..?

Respected Professor's i hope you are doing well and happy. i need some information about carbon Nanotubes. before blending the CNT with the matrix the CNT has been introducing in some treatments....

24 February 2021 5,383 5 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