[gmx-users] Exploding box after 55.5ns of simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 30 21:12:21 CET 2007

> tcoupl          = berendsen
> tc-grps         = protein SOL CL-
> tau_t           = 0.1 0.1  0.1
> ref_t           = 300 300 300

Bad idea.  Never couple solvent and ions separately.  This is well-documented in
the wiki and on this list.  I experienced a similar explosion problem long ago,
and it turned out that my ions accelerated and shot out of the system.  It
happened early in the simulation, so I don't know if that is your problem or
not, but in any case, you should definitely couple the solvent and ions
together, i.e. tc-grps = protein non-protein


> Thank you,
> JW
> --
> JW Feng
> Ph.D. Candidate
> Center for Computational Biology
> Washington University in St. Louis
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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