[gmx-users] question on system blow-up

[Lei Qian]

Hi John,

Thank you very much for your reply.

After checking my log file, it seems my Metal ion cannot form a stable
coordination bonds in simulation.
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms 1180 1572           global  1180  1572
The number 1572 is my metal ion. And 1180 is an atom close to it in space.

Because it says "the first 10 missing interactions", but the file only
shows one missing interaction here LJ-14 atoms 1180 1572. It seems strange.
When I checked the trr file, the metal ion position shift away from its
normal position.
I will try to redo mcpb process.


On Fri, Sep 20, 2019 at 6:22 AM John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> Hi,
>
> > 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?
>
> Best,
>
> John
>
> >
> > Thank you!
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