Problem in energy minimization using Fixatoms or Constraints

From: Ranyere Deyler (
Date: Tue Mar 30 2010 - 12:52:09 CDT

Hi, sorry for the way i'm sending this email, but responding properly wasn't
working. I tried twice and nothing came. So i just pasted the three messages
here, in order to understand whats going on. So if someone could help me i
would appologize.

Well, thanks for your help. Using constraints didn't help so much. Well,
didn't have problem with the energies and i could see de .dcd file on VMD,
what i couldn't do using FixAtoms. Well, i used the follow:

constraints on
consref colunas.pdb
conskfile colunas.pdb
conskcol O

And seeing the .dcd file, i could see that the atoms of the columns didn't
get fixed. It messed up all the columns. Then i try using a different
sacling, such as
constraintScaling 5
But did no good either. I don't know if i'm doing it right, this pdb i used
is the same one that has the water, but i set the O columns to 1. I don't
know if that's enough for this.
So my problem now is, using "Fixatoms", it doesn't run properly, it runs
until the end, but shows indetermined values when it's running, so id
doesn't even build a proper dcd file. And if i use constraints, it runs
well, the dcd file is well built but the atoms i needed to be fixed were

So, i need some way of keeping the atoms of the columns fixed. Does any one
can help me doing this? Thanks a lot

Ranyere Deyler Trindade

On Wed, Mar 17, 2010 at 2:27 AM, Chris Harrison <> wrote:


What happens if you use "constraints" instead of fixedAtoms? Try:

constraints on
consref yourFixedAtomsPdbFileName
conskfile yourFixedAtomsPdbFileName
conskcol O

This will apply constraints with a weak force constant of 1kcal/mol to the
atoms. Does this fail as well?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Tue, Mar 16, 2010 at 12:45 PM, Ranyere Deyler <> wrote:
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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