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

Which is the most efficient etching solution for nickel based alloys?

Which solution reveals the microstructure and features of nickel-based alloys?

02 March 2021 2,221 3 View

Which is the most convenient manufacturing software for Additive Manufacturing?

Which tools can be used to generate machine codes for additive manufacturing?

02 March 2021 7,220 2 View

Could not amplify CD28 and CD3z ectodomain from cDNA of Jurkat Cells ?

For my experiments, I have to express ectodomains of human CD28 and CD3z. As a source, I extracted RNA from Jurkat cells and verified the quality of RNA on the gel. I, then, prepared cDNA using...

23 February 2021 7,051 4 View

How do I apply continuity boundary condition at the edge using form assembly in comsol?

The continuity boundary condition is automatically created for a shared (common) surface boundary but I want to have it for an edge. Please help me out. In image 8 is the base of the cylinder and...

05 February 2021 3,459 2 View

Direction 1 Vector in porous media ansys fluent ?

anyone can help me to explain what is direction Vector 1 and direction Vector 2 in porous media when modelling in ANASYS fluent

01 February 2021 6,866 1 View

What is the correct way to apply a Design effect for sample size calculation when the sampling method is linear systematic random sampling?

When we are doing sampling by means of simple systematic random sampling,how do we calculate the design effect for use during calculation of sample size for our work?

20 January 2021 5,328 3 View

Any reference to learn numerical methods for Viscoelastic compressible fluids(oil) (CFD)?

I am developing a solver to simulate compression of oil in shock absorber filled with viscoelastic compressible oil. The model will consider the loss due to viscosity which will decide the...

15 January 2021 1,707 1 View

No title

11 January 2021 3,284 3 View

Mauchly's Test is used for sphericity in RM ANOVA. Instead, can we apply Levene's test on the differences between all combinations of related groups?

sphericity test in Repeated Measures ANOVA

05 January 2021 6,177 4 View

Why Austenite grains in steel show much more twinning than ferrite grains?

It is oftentimes said to be a distinctive metallographic trait that differentiates a fully austenitic and a fully felly ferritic steel without etching that might distinguish between two. Why...

02 March 2021 728 2 View

Energy minimization in LAMMPS using NVT ?

How do I do energy minimization in lammps with NVT ensemble ? I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search...

01 March 2021 2,294 3 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

How to search for crystal structure for material with atomic position labelled?

I am using the crystallographic open database and materials project to search for cif file but the exact structure is not mentioned or how can I deduce that the given structure and atomic position...

23 February 2021 6,723 2 View

How to generate AA6061 alloy or any aluminium alloy crystal in material studio?

I need to carry out molecular dynamics simulation on Aluminium alloy. For this i need the crystal structure that which could be further replicated to form a structure.

22 February 2021 1,410 1 View

Build an orthogonal box in ASE?

Hello, I was wondering the best way to build an orthogonal box filled with a defined crystal structure in ASE. I know it could be easily done in LAMMPS, but I guess it is also doable in ASE. The...

21 February 2021 5,899 4 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View

How to raise temperature in small increments during equilibration in LAMMPS?

All, I am trying to equilibrate an Ice 1h crystalline structure to 250K in LAMMPS. When I tried to do this at 250K directly, the structure lost it's crystalline shape and became disordered post...

14 February 2021 5,747 2 View