Re: AMBER: Problem with Water solute during MD

From: Bill Ross <>
Date: Tue, 9 Nov 2004 09:36:22 -0800 (PST)

> My problem is, that the MD crashes without Error
> but with a coredump.

Usually there is a system msg to the console, like
'floating point divide by 0'. In batch mode these msgs
can wind up in a file.

> If I fix all the Water molecules with iBelly, the MD-run
> seems to work properly.

Did you minimize the system 1st and warm gradually? See
the equilibration faq if you haven't read it yet.

If shake is off, waters can fuse and explode :-)
since the H's are just within the vdw of the oxygen.

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Received on Tue Nov 09 2004 - 17:53:00 PST
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