Fixatoms minimization problem!!

From: Ranyere Deyler (
Date: Tue Mar 16 2010 - 12:45:57 CDT

Dear NAMD users.

The first time nobody could hep me, but now i've got a more especifc
problem. It's simple, i try to run a minimization in a system that is just
some atoms aligned forming columns. I made some columns side by side at a
reasonable distance between each other. So i fix them, by putting 1 on the
ocupancy column on pdb file. So i run NAMD, and it runs until the end, but
when i open the dcd file on VMD it shows nothing, and looking at Energys
while the NAMD is running, at all steps shows basicly the same results:

ine 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

The energy, i supose, it's getting indeterminate or something, so it's not
building the trajectory. And i don't know what could be.. It's just simple
atoms in columns, with no bonds, and i just fixed them. And turned the
"Fixatoms" on at NAMD parameter file. First i was trying with water on top
and on bottom, but there were errors, so i tried to run just the fixed
columns, and yet, with all kind of atoms, and even with big distance between
the atoms is still getting those erros. Anyone has any idea?? Thanks a lot.

Ranyere Deyler Trindade

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