Thanks, Timothy.
Before starting the QM calculation, I equilibrated the system for 600
nanoseconds. I have visualized the QMMM trajectory in VMD, and I observed
that the residue is getting broken after 1 ps and behaving abruptly. Could
you suggest a solution for this issue?
On Tue, Aug 6, 2024 at 7:28 PM Timothy Giese <giese025.rutgers.edu> wrote:
> You're going to have to open the trajectory in VMD and look at what is
> happening to the QM atoms. You are seeing vlimit (velocity too large)
> warnings and then a "box too small" error. This typically happens when the
> QM region "explodes" because there was a bad contact (for example, some
> hydrogens do not contribute to the LJ potential which can cause a coulomb
> catastrophe) or incorrect input settings. This will only become apparent
> to you upon looking at the trajectory.
>
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Received on Tue Aug 06 2024 - 07:30:02 PDT
