On Sat, Nov 01, 2025, Surabhi Singh 24933024 wrote:
>Thanks for the quick response, so I have checked there are no bad contacts
>or bonds reported by checkstructure.
Did you look at a simulation that was set to stop right before the first
vlimit message in the mdout file?
Run an initial simulation that stop a few steps before the first vlimit
message. Than continue (restart) from there, setting ntpr=1. Look closely
at the energies that are reported -- I suspect(!) that the electrostatic
energy will start to look odd, and using cpptraj checkstructure on a
snapshot right at the first vlimit error might reveal a bad contact. That
might at least get you started on finding the origin of the problem.
...dac
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Received on Thu Nov 06 2025 - 09:00:02 PST
