AMBER Archive (2006)

Subject: Re: AMBER: problem at the start of heating up (using extra-point)

From: David A. Case (case_at_scripps.edu)
Date: Sun Dec 03 2006 - 16:04:25 CST

On Sat, Dec 02, 2006, Rachel wrote:

>
> vlimit exceeded for step 0 ; vmax = Infinity

My guess is that you may have a "extra point" atom with zero mass, but that it
is not be recognized as an extra point. Hence, sander is trying to make a
velocity out of it, dividing the distance moved by the (zero) mass, and
getting infinity. You could check this by running a short test case with
finite masses for all atoms (including EP atoms), and seeing if the error
changes or goes away.

> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 49969 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 49969 0
> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 6328 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 6328 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 13725 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 13725 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 8660 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 8660 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 25765 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 25765 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 16154 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 16154 0

The fact that the "before" and "after" numbers are all the same is suspicous.
You may have to add debug statements to the code to make sure that items
that should be extra points really are.

....regards...dac

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