Could anyone point to molecular mechanics force fields for selenium nanoparticles?

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Could anyone point to force field parameters for phosphorothioate oligonucleotide??

I am interested in simulating RNA/DNA with phosphorothioate backbone. I am aware of the old parameters in AMBER force field. Could anyone point to recent publications or force fields to perform...

04 May 2019 2,906 2 View

How to apply position restraints for carbon nanotubes in GROMACS?

I am running a system with protein and carbon nanotube using GROMACS 5.1.4. I used position restraints for carbon nanotube however, during NPT run (both protein and carbon nanotube fixed),it...

09 October 2017 1,493 3 View

How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying to simulate...

09 October 2017 4,206 2 View

Does anyone have parameters for carbon nanotube (CNT) in AMBER package format?

There are many papers on MD simulations of proteins with carbon nanotubes using AMBER force field. I was wondering if anybody can provide parameters (frcmod or lib files) for carbon nanotubes in...

07 August 2017 557 1 View

How to calculate number of Nanoparticles given wt/wt %?

I know the size of nanoparticle and number of lipids in system. A 5nm gold nanoparticle has ~4000 atoms. A paper suggest lipids:Au ratio = 0.98 % wt/wt. How can I calculate the number of gold...

06 July 2017 5,680 2 View

How to deal with water bubbles during NVT runs with position restraints in a molecular dynamics simulations??

I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...

02 March 2017 1,249 2 View

How to build (replicate) lipid monolayer systems using gromacs?

I have a pdb file of coarse grained lipid monolayer system consisting of 64 DPPC lipids. The pdb file is missing box information. I am interested in simulating nanoparticle penetration in...

01 February 2017 2,732 1 View

Simulating chitosan using Glycam force field?

Is there any publication reporting simulation of chitosan using Glycam06 force field?

11 December 2016 2,121 0 View

What is the stereoisomerism in divalen cross-links found in collagen?

I was wondering if anybody has worked with chemistry of these two cross-linkers and have characterised by FTIR or MS whether they are cis/trans or S/R isomers? Apologies: I am not a synthetic...

08 September 2016 8,660 4 View

Anybody acquainted with simulations of hydroxyapatite surfaces in AMBER?

Dear list, I am trying to simulate protein unfolding on hydroxyapatite surface using AMBER MD package. I got the parameters for HAP (based on the interface force field). I prepared the system...

07 August 2016 6,889 0 View

Hello researchers Is this a random laser or just fluorescence?

I am using Rhodamine6G as gain medium and silver nanoparticles as scatterers on a microscope slide and laser input 532 nm comes from above.

09 August 2024 9,894 2 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Stability of the Solar System: Insights from Einstein’s Equations ?

The stability of the Solar System is a complex subject that blends the classical framework of Newtonian mechanics with the modern insights provided by General Relativity (GR). Understanding this...

07 August 2024 2,569 1 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

Binder for ZnO nanoparticles in graphite paste electrode?

I have been using paraffin, but the deposited ZnO still detach from electrode. What is the best binder to modify graphite paste electrode with ZnO nanoparticles?

03 August 2024 4,624 3 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Can i quantify a nanoparticle encapsulated in cell culture medium by hplc?

Hello, if you made a transwell assay where you incubate the cells with a nanoparticle-encapsulated drug and considering that in the oposite compartment you'll have both the free and encapsulte...

03 August 2024 2,730 1 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View