AMBER Archive (2008)

Subject: Re: AMBER: segmentation fault when restarting periodic structure

From: David A. Case (
Date: Tue Nov 18 2008 - 08:20:41 CST

On Fri, Nov 14, 2008, Diddo Diddens wrote:
> I would like to run an equilibrated structure (generated by another MD
> program) consisting of 100 DME molecules with periodic boundary conditions. I
> created a pdb file of the wrapped structure and created the .inpcrd file with
> xleap. An in vacuo simulation of a single DME molecule works well, pbc
> simulations from the tutorials as well. For some reasons AMBER gives a
> segmentation fault. Is it crashing because the molecules are not put together?

It is not possible to tell without being able to actually try things. My
guess is that the periodic boundary condition setup is not correct -- you
don't say how you did that -- just "created the .inpcrd file with xleap". You
probably need to post the exact procedure you used, and the relevant files.
We generally can't track down a segfault without being able to reproduce it.

Regular readers of the mail-list will recognize a common theme in reporting
problems: please report what you actually did ("typed the following into
xleap:..."), and not only what your intent was.


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