Dear AMBER users,
I would like to ask for suggestions regarding a possible connection between
some earlier observations in my *membrane protein–peptide simulations *and
the equilibration instability issues that I am currently encountering.
In earlier equilibration attempts, I completely removed the peptide
restraints and continued the simulation protocol. During those runs, I
observed that the distance between the peptide ligand and receptor
gradually increased over time despite being positional restrained on the
ligand and protein.
Additionally, while visualizing the trajectory in VMD, I noticed
significant deformation of the simulation box. The box appeared to become
increasingly elongated in one dimension while shrinking in another
dimension during the trajectory.
Initially, I suspected these effects might be related to artifacts or
normal membrane fluctuations. However, when I continued the equilibration
further, the simulations eventually failed with errors such as:
*"vlimit exceededCoordinate resetting cannot be accomplished.deviation is
too large."*
This makes me wonder whether the earlier ligand–receptor separation and box
deformation behavior were actually early indicators of system stability
issues.
I would greatly appreciate any suggestions regarding:
- whether such box deformation behavior is expected during membrane
equilibration,
- Whether this may indicate instability in membrane equilibration,
- and how to systematically troubleshoot this type of issue in AMBER
membrane simulations.
Thank you very much for your time and help.
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Received on Thu May 21 2026 - 03:30:03 PDT
