[gmx-users] question on system blow-up

Lei Qian tuk04130 at temple.edu
Fri Sep 20 08:06:38 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?

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)"

Thank you!

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