How to perform Brownian dynamics simulation with gromacs?

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What are the fundamental ideas of Monte Carlo dimensionality estimation, compared to Rasch residuals PCA?

I read an interesting article from Christensen (2007): A Monte Carlo approach to unidimensionality testing in polytomous rasch models. But do you have some further thoughts or maybe other...

08 August 2024 4,245 0 View

How to quantify polystyrene microplastic (8 micron) bioaccumulation in fish tissue?

"I have treated adult zebrafish with 8-micron polystyrene microplastic and want to study the bioaccumulation in different organs. Can this be done using hydrogen peroxide digestion followed by...

05 August 2024 853 3 View

In the presence of VERY high concentration (1000 ppm) of silicon, the adsorption isotherms of arsenic are showing anomalous trends, why so?

I conducted an adsorption experiment of arsenic on soil in the presence of different doses of silicon as competing ions to see the effect of silicon on arsenic adsorption and desorption. I took 5...

03 August 2024 6,500 3 View

Can Langmuir constant related to bonding energy (Kl) and Freundlich exponent (1/n) indicative of ads intensity show opposite trends with temperature?

The adsorbate is Arsenic and the adsorbent is a soil

18 July 2024 332 8 View

How can we calculate the polygon scanner speed by changing the supply voltage?

I am using a polygon mirror scanner that have 6 facets and the dc brushless motor speed was given 10,000 RPM. Now I want to know how to calculate the polygon speed if I change the power supply...

11 July 2024 5,942 1 View

How to give excitation to Crossed Dipole Antenna in HFSS?

I'm attempting to simulate a crossed dipole antenna. For excitation, I've placed a lumped port along each dipole. However, the resulting radiation pattern is similar to that of a single dipole....

08 July 2024 1,876 3 View

Does anyone know if there is a lab scale encapsulation machine available for purchase?

05 July 2024 3,888 1 View

How to troubleshoot error E1 on Biorad Powerpac Basic despite using sufficient and fresh buffer?

I have used this BIorad Powerpac Basic for 4 years now, before which it was used for another 5-6 years. Generally we addressed the E1 error by compensating with fresh buffer and/or filling the...

01 July 2024 7,104 1 View

How to explain the plot from gmx clustsize?

I am doing md simulation for protein aggregation. For doing cluster analysis I was trying with gmx clustsize. Now the plot that I am getting, can not find a proper explanation. With -hc flag the...

24 June 2024 5,245 0 View

Do you publish undergraduate research papers?

if yes, is the publication free of charge

06 June 2024 4,270 1 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

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

Z-average size from Dynamic Light scattering can it be lower than the original probe size?

Hi everyone, Recently I have been conducting Dynamic Light scattering experiments in a micellar solution at 5 and gel at 37 degrees of Celsius with latex particles of diameter 190-500 nm. While...

01 August 2024 1,168 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 780 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 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 672 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

I found the zeta potential of exosomes in DLS and it was -8mv. So is it correct or not ?

What should be the zeta potential of bovine milk exosomes

25 July 2024 7,376 5 View