Yunus Emre Dilek

3 Questions 3 Answers 0 Followers

Questions related from Yunus Emre Dilek

Is it possible to write a PDB file inside an NAMD configuration file?

I'm doing several steps, such as minimization and equilibration, to start running MD simulations and I'm trying to automate this process by running one step after finishing the other. When I go...

11 February 2024 7,766 1 View

How to keep the trajectory in place after PBC wrapping using VMD?

I have a protein embedded in lipid bilayer. At some point, my protein moved towards the edge of simulation box. I applied PBC wrapping so the box is centered around protein. However, the...

30 December 2023 2,066 0 View

What is the script for hinge angle calculation using 3 center of mass values in VMD?

I have a protein simulated. I want to measure the angle between two domains (domain II & IV) and use the third domain (domain III) as a hinge between them. First, I want to select center of...

25 February 2022 2,887 3 View