Re: Fixatoms minimization problem!!

From: Chris Harrison (
Date: Wed Mar 17 2010 - 00:27:37 CDT


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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:54 CST