Büşra Sevim

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Questions related from Büşra Sevim

Disulfide bond loss at high temperature in MD simulation?

In MD simulation, I see that the peptide loses its disulfide bond as a result of high temperature application. I can't see the disulfide link in PyMOL, but I can see a link with the SG code in the...

16 April 2023 3,584 1 View

How can I fix GROMACS genion error?

I follow the protein-ligand simulation tutorial protocol. For my own protein-ligand simulation, I give the following commands at the ion addition stage: gmx grompp -f ions.mdp -c solv.gro -p...

05 January 2022 9,327 1 View

Is there a method by which I can analyze the conformation of proteins at various temperatures in silico?

I want to analyze the responses and conformational states of proteins at various temperatures in silico. Can I do this with molecular dynamics simulation programs like gromacs? Is there a special...

11 December 2021 7,497 3 View