AMBER Archive (2005)

Subject: Re: AMBER: Minimization of avg structure-SANDER Bomb

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Mar 17 2005 - 13:01:33 CST

> I was trying to minimize an average structure with BOX info....got from
> Ptraj (as a restart file), but the following error occurs:

Have you looked at the average structure? My guess is that if you have
BOX info, you averaged the solvent/ion positions along with the solute
structure which will lead to a large blob of overlapping molecules at the
center of the box due to rapid water/ion diffusion. In general, it is
meaningless to coordinate average the solvent since its motion is rapid.
This could lead to the blow up of the non-bonded pairs (since you
effectively have many more molecules within the cutoff than would be
normally expected).

What you have to do, if you want to minimize a solvated average structure
is strip the water and rehydrate or use an implicit solvent to do the
minimization (or minimize in gas phase)...

--tom

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