Hi Callum,
Thank you for your response and for the helpful suggestions.
I wanted to mention that I was already using the semi-isotropic barostat
parameters you suggested:
ntp=3, csurften=3, gamma_ten=0.0, ninterface=2
Unfortunately, I am still encountering the issue and have not yet been able
to identify the underlying cause. I am continuing to investigate the system
setup and simulation protocol to determine what might be contributing to
the instability.
Thank you again for your time and for the recommendation. I appreciate your
help and will keep working on troubleshooting the problem.
Best regards,
Arti
On Thu, May 21, 2026 at 6:41 PM Dickson, Callum <callum.dickson.merck.com>
wrote:
> 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.
>
> EXTERNAL EMAIL– Use caution with any links or file attachments.
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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 Sat May 30 2026 - 09:00:02 PDT
