Problem in minimization, Energy "-1.#IND" and bad dcd file.

From: Ranyere Deyler (
Date: Sun Mar 14 2010 - 17:36:19 CDT

(SOrry for the first mail, i accidentaly sent it before it was ready, my

Dear NAMD Users,

I'm having some problem with a system i'm working on. It's basicly looks
like the "Water in nanotubes" of the tutorial, but instead of the nanotubes
i'm using columns of atoms, it's columns of the same atom. So i put them
with a reason separation, and them i add the water on top and Bottom. When i
try to minimize it runs just fine, and goes until the end, generating all
files. But when i try to look the psf together with the dcd file on VMD, it
shows nothing. And Taking a look on the run, i could see some lines like

Line minimizer bracket DX -1.#IND -1.#IND DU 0 0 DUDX -0 -0 -0
Energy: 99 0.000 0.000 0.000
               0.000 0.000 0.000 0.000
               0.000 -1. #IND 0.000 0.000
              -1. #IND -1. #IND 18050.00 -1.#ind

So, i'm using it on windows. And i was wondering if this is the same as the
"NaN" in others errors.
So i don't know what's happening. If someone could help me i'd appreciate.

Ranyere Deyler Trindade

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