Can anyone help me o build coarse grain model for metal oxide nanoparticles using GROMACS?

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How to set up pH?

I want to study the adsorption mechanism of citrate, oxalate, and pyrocatechol on hematite nanoparticles in the pH range of 9-5. Moreover, I want to study the presence of different electrolytes...

09 October 2018 7,260 3 View

How can I determine the size of the nanocluster?

I have created ZnO cluster in GaussView by increasing the lattice parameters in all three dimensions with total number of atoms as 32. Is it possible to know the size of this cluster from the...

02 March 2016 8,634 1 View

Any suggestions on simulating DPPC lipid bilayer using OPLSAA forcefield?

I am trying to simulate dppc lipid bilayer using OPLSAA forcefield. I downloaded 128-dppc.pdb, 128-dppc.top, dppc-opls.itp and opls-ua-lipid atomtypes.itp (contains only atom types) files from...

03 April 2015 5,915 5 View

Free version of CRYSTALMAKER SOFTWARE?

Is free version of CRYSTALMAKER software available for download? I downloaded demo version but that does not allow to save file.

03 April 2015 4,861 2 View

Can somone help with an error while creating topology file using topolbuild?

I converted the pdb file to mol2file using openbabel 2.3.2. When I am trying to execute the topology of the file using the following command: ./topolbuild -dir...

03 April 2015 5,464 12 View

Can anyone help me use martinize.py to generate coarse grain structure of a iron pyrite nano cluster?

I created iron pyrite nanocluster in material studio 7.0 and exported it as .pdb file. I downloaded martinize.py to convert this nanocluster to coarse grain and create simultaneously cg.gro and...

02 March 2015 1,485 4 View

I have installed GROMACS 4.6.5 and FFTW3.3.4. In the steps of installing FFTW, I also installed steps for Double Presicion Versio. What is this?

I am a beginner in the field of GROMACS.

01 February 2015 8,353 0 View

Could GROMACS be used to study cytotoxicity of metal oxide nanoparticles?

GROMACS

05 June 2014 2,024 1 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

Does the pressure(-600 mmHg) affects pH?

When I conducted the degassing experiment using decompression under anaerobic condition(and I used ferrous based chelating agent), the oxidized ferric were observerd. So, could you tell me the...

03 March 2021 4,892 5 View

I need to image mesoporous silica nanoparticles that are in ~100 nm size and do high resolution TEM to look at mesopores. what grids should I use?

Need to image mesoporous silica nanoparticles using the TEM. Also, need high resolution TEM images to see the mesoporous structure. Kindly suggest what kind of grids to use. Thanks, Shatadru

02 March 2021 1,787 2 View

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

Can chitosan alone can act as a reducing agent for Cu(0) nanoparticle sythesis?

[Synthesizing Cu nanoparticles without using chemical reductants]

01 March 2021 8,359 1 View

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 3 View

What is the state of the drug inside solid lipid nanoparticles (SLNs)?

I am a little confuse with the mechanism of solid lipid nanoparticles (SLNs). The main point of encapsulating drugs into SLNs is because some drugs have low solubility in water. Therefore, SLNs...

01 March 2021 3,703 3 View

How to check the uv-vis absorption of nanoparticle by surface plasmon resonance?

I try to check the uv-vis absorption of Indium nanoparticle. Now I am measuring in solution, can I measure it in the form of a film?

01 March 2021 930 3 View

Distribution of particles in metal matrix?

How would define the "good" and "poor" distribution of particles within the matrix. Is there a quantitative solution to assess the distribution of the particles, which then having denotation of...

28 February 2021 7,397 8 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