Hello,
I’m simulating a nanodisc membrane system.
My equilibration pipeline was: EM → NVT (posres) → NPT ((posres, released over 7 steps)) → NPT (free).
At each stage, I used -t to continue from the previous run and set -r to the latest .gro file from the previous step. The equilibration was completed, but I’m not sure if the restraint protocol was applied correctly. I noticed that in the CHARMM-GUI pipeline, they keep -r fixed to the initial structure and do not use -t during each equilibration step.
Since I used -t and changed -r at each stage, would you recommend repeating the equilibration before starting production?
Thank you very much for your guidance.