Calculating Water flux through AQP1 monomer in GROMACS?

More Mads Jepsen's questions See All

Why Do TDS and EC Increase with Larger Wastewater Volumes, While BOD and COD Decrease?

I have carried out MFC experiments on three different volumes, 50, 500 and 1000 mL of wastewater. Results after MFC treatment shows that TDS and EC are more in larger volumes of water i.e. TDS and...

09 August 2024 9,621 0 View

How to enrich pig excreta for increasing nutrient quality organically ?

Pig slurry is rich in major and minor nutrients. Is there any way to improve / Enrich its manure quality to be used in agriculture organically ? please share your knowledge.

09 August 2024 5,605 2 View

Is it possible to plot the atom-projected band structure using GPAW?

Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...

07 August 2024 269 3 View

Unusual intensity drop in some sections of chromatograms in DDA?

Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...

07 August 2024 3,218 4 View

Leaf area of tomato ?

Hi How can this equation Ln(LA) = 1.038 + 0.89 ln(X) be applied to calculate the leaf area of a tomato? Can you explain with an example and what is the substitution of Ln and ln?

06 August 2024 2,508 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

How to preform densitometry on SDS-page bands?

I ran a SDS-page of a bacterial lysate and I want to quantify protein concentration in a specific band. I was thinking of using a standards ladder or make some standards are different...

05 August 2024 9,805 3 View

XRD Analysis is showing only Calcium carbonate. It is not showing other compounds. Can anyone help me get the other compounds?

XRD Analysis is showing only Calcium carbonate. It is not showing other compounds. Can anyone help me get the other compounds

04 August 2024 3,019 3 View

Which solvent is better to dissolve with secondary metabolites extracted from fungi?

I work on MCF7 cell cell for anticaner purpose and I wa to do drug preperation the drug ( secondary metabolites extracted from Aspergillus) My question which solvent is better with these secodary...

03 August 2024 4,725 2 View

What are the limitations and challenges of using machine learning for predicting concrete compressive strength in practical applications?

Machine learning (ML) has shown great potential in predicting the compressive strength of concrete, an important property for structural engineering. However, its practical application comes with...

03 August 2024 2,546 2 View

• What the possible Persistent Organic Pollutants and Heavy metals present in fluorspar, sediments, and water bodies around its mining area?

Approximate concentrations are require in compared with the WHO permissible limts

11 August 2024 2,723 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Do interactions between biosphere, carbon cycle, & water cycle impact global warming & interaction between atmosphere & hydrosphere?

How do interactions between the biosphere, the carbon cycle, and the water cycle impact global warming and interaction between the atmosphere and the hydrosphere?

09 August 2024 3,291 2 View

Is it true that $\det(V(A))$ may be only $\pm 1$, depending on $n$, for the last symmetric tridiagonal matrix $A$?

One can try to generalize the Vandermonde determinant in the following direction: Let $A$ be any symmetric $n$-order square matrix. Consider its powers' diagonal elements $(A^k)_{ii}$ and...

08 August 2024 6,690 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

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

What should I do with parameters that are not relate to my simulation in MyLake model?

I want to Estimate surface heat fluxes using MyLake, but I don't have all the initial values in model parameters section and other sections,is there a way?

04 August 2024 1,537 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

Budheswar Dehury

Stéphane Abel Could you please elaborate a bit. How can you compute the water permeability through the pores of Aquaporin?

Stéphane Abel thanks a lot for your kind input and suggestion. The g_count is not compatible with the new xtc and tpr files. Could you help me in getting the write command to execute? I have generated the trajectory using GROMACS 2019.3 version and CHARMM36m forcefield.