What is the difference between surface and bulk solution? Which one is more polar?

Hi, What is the difference between surface and bulk solution? Which one is more polar? does it depend on the characteristic of surface? Since ZnS surface(nano sheet) is partly hydrophobic, so...

31 December 2018 8,557 7 View

How show in ball and stick view by OVITO?

Hi, How show in ball and stick view by OVITO? Best

31 December 2018 8,262 1 View

Problems with g_dist?

Hi, my system contains 30 same molecule around nanotube. each molecule is in 2nm far from nanotube. i want to know how this distance change during simulation time. I have attached the same...

11 December 2018 5,243 1 View

How calculate adsorption number of molecule in molecular dynamics simulation?

Hi, My system contains 20 amino acids around nanotube. I want to know the adsorption amount of AA DURING simulation time; the adsorption occurs when the distance between one of non-hydrogen atoms...

10 November 2018 1,644 6 View

Is it rational to freeze/constraint bond in absence of kb for forcefield parameter?

Hi, I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond, Mn-O bond,... formed. Now i want to do MD simulation for this functionalized nanotube. (I use AMBER99SB ff) How should...

08 September 2018 1,873 6 View

How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

Hi, How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation? I did simulations by GROMACS, is it...

08 September 2018 5,160 3 View

How can i calculate the distribution of water polarization above surface?

Hi, I study the interaction(calculating PMF for different distances of molecule above surface) of amino acid with surface in presence of water( using TIP3P water model, AMBER force field by...

08 September 2018 6,851 7 View

How define Mn in AMBER forcefield?

Hi, I have Mn in my strucrure and i want to use AMBER forcefield in GROMACS. But it is not defined in atomtypes. What should i do exactly? Best regards

08 September 2018 1,296 5 View

How functionalize ZnS nanotubes with different organic and inorganic molecules?

Hi, There are many studies about functionalizing different ZnS nanostructures. but i couldn't find anything about ZnS nanotube. Is it possible, at all? would you please share me your...

08 September 2018 3,161 9 View

How prove the formation of bond during optimization?

Hi, I do molecular dynamics simulations and new in quantum calculations. Recently i studied the interaction of amino acid with ZnS nanotube by DMOL3 and i wanted to know that does any bond formed...

08 September 2018 2,414 6 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 get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does anyone know to clarify these changes?

01 March 2021 1,290 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 convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 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

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

How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials?

Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...

25 February 2021 9,936 2 View