Re: "gradient tolerance" for minimization

From: Jim Phillips (
Date: Thu Jul 22 2010 - 14:52:07 CDT


The reported gradient value is along a non-normalized search vector, so
its magnitude is not physically meaningful. Even if it was, it probably
wouldn't be quite what you want, since it only takes one large force to
kill a simulation. Specifying that all net atomic forces are below a
certain value would accomplish that, although that would need some
additional control logic to stop minimization ahead to schedule.

My philosophy has always been that if a thousand steps of minimization
isn't enough to start equilibration, then a million won't be either.


On Thu, 22 Jul 2010, Parisa Akhski wrote:

> Dear NAMD users,
> I am using NAMD to run MD simulation on a DNA system. To the best of my knowledge, in order to check if the minimization is OK, the gradient tolerance should be checked until it drops below 1.0.
> I cannot find the "gradient tolerance" in my output file. The only thing I found is
> "LINE MINIMIZER REDUCING GRADIENT FROM # TO #" in which # are two different numbers.
> 1. Can this information be used to find the "gradient tolerance"?
> 2. Is "gradient tolerance" the difference between these two numbers?
> 3. Is this the only item that should be checked to evaluate whether the number of steps are enough for minimization?
> I really appreciate your help in advance,
> Parisa

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