Does anyone have CHARMM potential for simulating the interaction between Ag/Au nano particles with protein?

08 May 2020 0 8K Report

I am trying to simulate interaction of hemoglobin with silver and gold nano particles using NAMD. However, I couldn't find any suitable potential. Does anyone have any idea to simulate the protein-nano particle complex using NAMD? or should I switch to gromacs?

Badges
Science method

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

What is Nano technology with coronavirus helpe the human..and is it nano mterals removal of covid19?

I anwar by adsorption or reaction ..but it is either more method...

02 March 2021 4,811 2 View

How to compare different concentrations of nanoparticles for characterization from ICP-MS?

I took measurements of different concentrations of 15 nm and 5 nm Au nano particle solutions. I'm trying to determine which concentration I measured gives the best reading overall. I also...

02 March 2021 7,626 1 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

LEDs on Vis Light photo degradation of MB water sol via N doped TiO2 in a mini flume?

Good day to all, I have no experience with light emitting diodes. I am building a glass mini flume to demonstrate the photo degradation of Methylene Blue in water running over self cleaning...

26 February 2021 4,026 5 View

Zno nano particles colour changed from white to grey in process of calcination any suggestions?

In the formation of Zno nano particles process, after drying at 120 degree C, my zno nano particles are completely white but when i calcine it for 450 degree C it converts into grey colour. i...

26 February 2021 2,435 4 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

What is the best solvent to remove PDMS from nano particles?

I want to remove PDMS oligomers from the surface of nanolayers. I have just read a very helpful paper about the compatibility of PDMS with different solvents( Solvent Compatibility of...

24 February 2021 7,845 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