Hi,
Regarding the “vlimit exceeded” error, this normally indicates close contacts / high energy starting coordinates. An easy way to check for this is using the cpptraj “checkoverlap” command.
Regarding the specific question of deformation of the simulation box, with long MD timescales it has been seen that membrane simulations boxes can contract in either the X- or Y- dimension using the isotropic barostat, resulting in a thinning along one dimension. I would recommend the semi-isotropic barostat (which couples the X- and Y- dimensions), like this:
ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,
Best regards,
Callum
From: Arti 2410204 via AMBER <amber.ambermd.org>
Date: Thursday, May 21, 2026 at 06:15
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Vlimit exceeded, box deformation, ligand receptor distance change.
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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 - 06:30:06 PDT
