GROMACS version: 2022.6
GROMACS modification: Yes/No
Hello everyone,
I am relatively new to gromacs and just learning about Molecular dynamics. I am trying to unfold a mutant and wild-type version of a protein(~574 aa) to understand its thermostability in a water box over time. What approach will be the best for me
- Umbrella sampling
- simulated annealing: Increasing its temperature to around 400 K and doing a production run.
My other query is, do i have to do the NPT and NVT equilibriation at 300K or 400K and do i need to restrain the whole protein during the equilibriation as well as production run to unfold it. Apologies in advance if my question isn’t scientifically sound. I am attaching the .mdp files. Please take a look. Any suggestions would be helpful
NPT.mdp (3.0 KB)
NVT.mdp (2.4 KB)