AMBER Archive (2009)

Subject: Re: AMBER: energy jumps during molecule minimization

From: David A. Case (
Date: Fri Jan 02 2009 - 06:48:23 CST

On Thu, Jan 01, 2009, Paul Ledbetter wrote:
> I have been experimenting with changing force field parameters for a
> model of a relatively small molecule (22 atoms). For some choices of
> parameters, I see very strange results during minimization.
> Specifically, the energy of successive geometries during the
> minimization will sometimes jump to a higher energy than the starting
> geometry. This happens with greater probability as the number of
> cycles increases. I have set the non-bonded cutoff to larger than the
> system, so I am unable to think of a good reason for this to happen.
> I have included an mdout from one particular run. Any advice would be
> appreciated.

This is part of the nature of the conjugate gradient routine used. You
should set ntpr=1 to see the details of what is happening. Also, the
"xmin" (ntmin=3) will generally give a smoother and faster minimization


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