From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Mar 17 2010 - 00:27:37 CDT
What happens if you use "constraints" instead of fixedAtoms? Try:
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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Tue, Mar 16, 2010 at 12:45 PM, Ranyere Deyler <ranyere_at_gmail.com> 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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