Re: Maximum Velocities

From: Eric H. Lee (
Date: Tue Jul 08 2008 - 13:50:51 CDT

You can also perform energy minimization in namd, which should help
with your velocity issue. Simply add the line: minimize XX where XX
is the number of timesteps you wish to do the minimization. The NAMD
tutorial has more details.


On 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.

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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