Re: Fixatoms minimization problem!!

From: Ranyere Deyler (
Date: Mon Mar 29 2010 - 18:41:29 CDT

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

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

> Ranyere,
> 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
> --
> 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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