[gmx-users] question on system blow-up

John Whittaker johnwhittake at zedat.fu-berlin.de
Fri Sep 20 12:22:35 CEST 2019


> Dear gmx-users,
> Could I ask a question on system blow-up? Thanks!
> I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found
> system blow up at around 1ns. ("atoms involved moved further apart than
> the
> multi-body cut-off distance")
> When I checked the trajectory files: nvt.trr, npt.trr, I found the
> distorted water molecules (very very long H-O bond), although protein
> looks
> OK in these traj files. I guess perhaps those distorted water molecules
> are
> blow-up and they can gradually affect protein?

It doesn't matter which molecule it is; if a molecule is blowing up, it
will cause the simulation to fail. After visualizing your system, are you
able to see what causes the elongated H-O bond? Are molecules overlapping?
Are there other warnings (like LINCS warnings) in your output? You need to
provide some more information about the system you are simulating or no
one will really know how to help.

> I tried to change production npt setting to nvt (pcoupl = no), and change
> integrator md to sd, change tau_t: 2.0 2.0. However, the following error
> always show up:
> "1 of the 20067 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.18213 nm) or the two-body cut-off distance (1.241 nm)"

These settings are likely not the cause of your problem and they probably
wouldn't change much about the simulation consistently blowing up. When
you make these changes, are the same molecules distorted?



> Thank you!
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