Can anyone provide guide to carry out cfd simulation of wavy fins in forced convection?

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

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

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

How to Import Blade geometry from CAD file in ANSYS design modeler?

Hello. I have the geometry of a blade in CAD file (stp) and I want to prepare the blade for meshing with turboGrid. I must import this file into designModeler and then transfer to the...

27 July 2024 356 3 View

How to create parameter and coordinate files for ligand in amber when FATAL error (maybe due to duplicate bond specifications) happens?

Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...

17 July 2024 3,472 3 View

How to define a zeolite structure with rigid framwork?

Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...

15 July 2024 4,590 1 View

How to generate average structure from an MD simulation?

Is there any post processing tools by which I can get average value of lattice parameters from cell trajectory? For example: I ran 'vc-cp' (CPMD) in quantum espresso (for Silicon) and Si.cel file...

08 July 2024 9,234 1 View

Why does our stiff biochemical ODE model in R produce unreasonable results (negative values, NAM) despite using solvers like lsoda, vode, and rk4)?

We have developed an ODE model comprising 25 interrelated equations with common coefficients. This biochemical model, applied in wastewater treatment, is characterized by stiffness. Utilizing the...

06 July 2024 7,077 4 View