Is RMSD enough to access the stability of the complexes?

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Can we mark 'EFL Learners shifting from general digital to AI technologies' as technological transition?

After COVID-19 it has seen that EFL learners technological affiliation has raised. In addition, in the post-COVID period learners started to engage AI technologies like ChatGPT while learning...

08 August 2024 8,964 4 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

Can I multiplex a mouse monoclonal and rat primary for IHC (mouse brain tissue)?

Hi all, I was just wondering if anyone has experience with multiplexing a mouse monoclonal primary and a rat primary. I'm trying to multiplex by incubating them in the same well but was told by a...

06 August 2024 9,710 1 View

How to convert g/kg Humic acid dose to kg/ha?

I used humic acid at 0.044 g/kg soil in my pot experiment. But finally, I have to recommend kg/ha. Each pot's soil weight was 11 kg. What is the solution?

02 August 2024 7,186 6 View

Bangladesh government's reported plan to use lethal force against protesters? We need help Urgently ?

Please Help Us Urgently

01 August 2024 711 1 View

"How has Leader Sheikh Hasina's government allegedly responded to student protests, including the reported killing of over 500 students ?

"How has Leader Sheikh Hasina's government allegedly responded to student protests, including the reported killing of over 500 students, as well as arrests, custody, remand, and the involvement of...

29 July 2024 2,181 7 View

Can a photocatalytic degradation of methylene blue from red mud be pseudo- zero order kinetics?

My photocatalyst from solid waste red med. Dye is methylene blue My all parameter study is showing zero order. How to prove it further that the reaction in zero order?

29 July 2024 7,404 1 View

How to calculate pseudo order kinetics?

I know the rate law. But for my photo-catalytic experiments, first 90min is adsorption (dark) and next 150min is under UV light (total 240min). How to remove the adsorption part for calculation?...

21 July 2024 8,807 6 View

How can I calculate spin texture using Quantum Espresso for non-colinear case ?

I want to calculate the spin texture for the electronic band structure obtained from SOC calculation. Is there any way for calculation of spin texture using quantum espresso??

19 July 2024 8,571 1 View

What is the average energy consumption per gate operation with superconducting qubit?

Could you provide information on the average energy consumption per gate operation when using superconducting qubits, specifically focusing on the microwave power required to implement gates? I...

15 July 2024 954 0 View

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View

RMSD of Protein ligand complex is higher than the apo form.Why?

I have performed a 100 ns md simulation for protein ligand complex .The result generated is found that the complex RMSD is higher than the Apo form.What could be reason for this ? Could anyone...

24 June 2024 9,049 3 View

What could be the possible reason of a sudden fluctuation in a stable RMSD plot of a protein-protein simulation?

I have run MD simulation of a protein-protein docked complex for 50ns. The RMSD plot obtained from the simulation is attached here. The RMSD plot shows a stable trajectory for entire simulation,...

09 June 2024 7,886 1 View

Comparison of three-dimensional structures obtained in Swiss-Model?

Good day! Please tell me, is it correct to compare two structures obtained using homology modelling on the SwissModel website and then compare them using RMSD in PyMOL?

18 May 2024 3,566 1 View

RMSD plot from GROMACS output file .xtc did not start from 0ns. How to get the 0ns frame?

Dear GROMACS expert, I am currently having trouble to analyse the results from my simulations. After processing the output files using this command, gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o...

02 May 2024 6,690 7 View

What is the best practices and presentation for analysis of multiple molecular dynamics simulations ?

Hi, I've noticed a common practice in publications where multiple Molecular Dynamics (MD) simulations are conducted with varying initial velocities. However, I'm uncertain about the appropriate...

18 April 2024 6,293 2 View

Reason(s) for the difference in RMSD of the Docked Structure and Co-crystal?

Aside from defining the disulfide bond, what other reasons could account for the significant difference in RMSD of the docked structure and co-crystal?

15 April 2024 7,706 2 View

How do I split my Autodock Vina pdbqt file into indiviadual comformation files on windows?

I want to calculate the RMSD for the individual confrmations from the output file pdbqt into to run in into a program that only accepts PDB files. I can convert pdbqt files to PDB using openbabel...

25 March 2024 3,075 5 View

VMD NAMD Plot?

Hello. How can I plot in RMSD H-Bond and radious gyrus in VMD in Windows? I ran MD in Namd and y I have all the files Step5.

23 March 2024 7,689 1 View