AMBER Archive (2002)

Subject: Re: BLOWUP after 100 ns???

From: Randy M. Wadkins (rwadkins_at_flash.net)
Date: Thu Sep 19 2002 - 20:41:16 CDT

>(Note that this is a blowup after about 100ps, not 100 ns...)
>
>There was a similar report on the reflector a short time ago. I'm a little
>suspicious of using the Berendsen temp. algorithm for a non-condensed phase
>system with a relatively small number of degress of freedom: one could get
>hot-spots in the molecule (I imagine) that might not be properly handled. But
>this is just a guess. We have run temperature regulated GB runs on smallish
>proteins (100 residues) for 10-20 ns without seeing behavior like this (yet).
>We do know that the igb=1 formula can lead very occasionally to excessively
>large effective radii, which can in turn lead to bad dynamics.
>
>It's also worth noting that the "sa" part of gbsa (as implemented in Amber)
>has some known "discontinuities" that disrupt energy conservation; see
>

Hi Dr. Case:

Of course this is 100 ps: brain not working when typing.

Anyway, I restarted the simulation and, as of this writing,
everything is going fine. Just a strange occurrence. I ran the
exact same simulation on the wt and another single residue mutant
with absolutely no problem.

Perhaps a computer hiccup?

--Randy