Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using molecular mechanics force fields?
I myself use gaff ff and resp charges for Se related species
Thanks Zhaoxi Sun. How about interaction with solvent and Se? What are the non-bonded parameters?
In GAFF you can have the vdw and RESP gives the charge
Zhaoxi Sun Have you simulated trigonal selenium cell?
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
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
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
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
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
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
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
Is there any publication reporting simulation of chitosan using Glycam06 force field?
11 December 2016 2,121 0 View
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
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
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
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
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
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
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
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
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
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
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
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