RE: AMBER: NAN errors

From: Ross Walker <>
Date: Tue, 25 Jan 2005 13:56:33 -0800

Dear Venkat,
> --------------------------------
> 1 nan nan 1.2155E+02 O 2351
> BOND = 1307.4974 ANGLE = 3088.3520 DIHED = 4822.5876
> VDWAALS = 1321392.7282 EEL = -76345.8040 EGB = nan
> 1-4 VDW = 3348.7754 1-4 EEL = 42319.0282 RESTRAINT = 0.0000
> -----------------------------------

The NAN comes from the EGB term which is the generalised born energy term
(igb=1). This means that something in the egb routine led to an infinite
energy. The error in this case, however, I suspect is still due to atoms
being too close together. Note your VDWAALS energy = 1321392.7282 This is
HUGE and almost certainly comes from two atoms being too close together.
They aren't so close that they lead to an infinite energy, hence the reason
the explicit water calculation worked, but they are close enough that it
leads to an error in the calculation of the generalised born term.

Either way, the fact that the simulation doesn't crash or give a nan during
the explicit water simulation does not mean it is correct. I suspect if you
look at the minimised structure it probably does not make sense. Also,
running MD on the system is likely to lead to an unstable trajectory.
Try checking all the distances in your system to see if any atoms are too
close together. Xleap should report close atoms if you use the check

Failing that you could try running a 100 steps of MD with your unminimised
structure. Write the mdcrd file every step (ntwx=1) and then you can
visualise it in something like VMD. It should be obvious what atoms are too
close together, they will fly apart rapidly. This will allow you to narrow
down where to look to fix the problem.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Jan 25 2005 - 22:52:59 PST
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