On Fri, Oct 31, 2025, Surabhi Singh 24933024 via AMBER wrote:
>I’m still stuck at the equilibration stage.
I'm unsure how far along your simulation has gone before you get a vlimit
error. Be sure that the minimization results look good. In particular,
use the "checkstructure" command in cpptraj to examine both your input
structure and the results following minimization. Try to correct any really
bad contacts or bad bonds it finds.
Does the vlimit error happen right at the beginning of some MD stage? If
so, use checkstructure on the input coordinates for that stage. If the
error happens part way through (as it seems to be from your email), run a
repeat simulation that will stop right before the first vlimit problem. The
examine that structure, both visually and with checkstructure.
....hope this helps...dac
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Received on Fri Oct 31 2025 - 16:00:02 PDT
