Berna Erdoğdu

5 Questions 4 Answers 0 Followers

Questions related from Berna Erdoğdu

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...

19 April 2024 6,247 2 View

Why are there no plaques visible in the double agar when using the filtrate obtained from the plaques observed in the previous petri dish?

I'm facing difficulties while preparing double agar using the bacteria I initially used to isolate my phage. I wanted to see how different concentrations of these bacteria (measured as OD 0.1,...

17 November 2023 5,747 2 View

How I can show the broad host range of the phage based on its genome with bioinformatics tools ?

Greetings, I have recently isolated a new E.coli phage and during the assessment of its host range, I discovered that this particular phage was effective against Pseudomonas aureginosa and...

30 June 2023 261 4 View

Why do water molecules and ions appear outside the simulation box during simulation?

Hi I am using Gromacs 2018 version. I ran the MD simulation for 400 ns at 300K (I didn't change the classic tutorial md.mdp except for nstep). While watching the .xtc file, I noticed that the...

20 May 2023 8,704 1 View

Some of my protein comes out of the box as a result of the simulation, is this a problem for the MD simulation?

The box size determined for my protein before starting the MD simulation is as in image 1. After 200 ns, some of the protein comes out of the box (image 2). Does this affect the simulation...

03 May 2023 3,908 3 View