Re: Maximum Velocities

From: Chris Harrison (
Date: Tue Jul 08 2008 - 15:33:19 CDT


Please try the following things and see if one fixes your problem:

1. minimize in namd (command is: minimize #_of_steps). Start by
trying a thousand or so steps.
2. make sure the temperature control is turned on.
3. try using one of the example simulations from one of the tutorials
with your .conf file (with appropriate alterations for filenames and
periodic box size). I would recommend starting with files from the
NAMD tutorial. The files are available on our website at:


On Tue, Jul 8, 2008 at 1:20 PM, Alejandro Ortega <> wrote:
> Hi everyone,
> I'm having trouble when I run my simulation in NAMD. I have a simulation of
> a water box, only. But when I run it namd tells me that simulation has
> become unstable due to atoms going too fast.
> I tried the command reinitvels but it doesn't work either. I think it has to
> be with the bond energies but I don't know what am I doing wrong. It also
> tells me that I have absolute/relatives imprecisions on the VDW table.
> I tried to minimize energies in the program Chem 3D with the tool MM2, but
> the program modifies the original PDB. What else can I do in order to
> minimize the energies of my molecules?
> Also, I noticed that the temperature doesn't seem to work on the
> configuration file, if I give a value of 100K, the simulation behaves the
> same as if I give a value of 500K,
> In conclusion, how could I correct the atoms velocities and the values of
> the VDW table? and does someone know why the temperature doesn't seem to
> affect my simulation?
> Any kind of help would be highly appreciated.

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

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