Re: Energy minimization at NAMD

From: Michael Grabe (
Date: Tue Jun 15 2004 - 16:55:01 CDT

Xin Chen,

I would look up a recent journal article and follow their protocol
before continuing. This will almost always include 200-1000 steps
of minimization before starting equilibration of the system.
I have no idea if you solvated your protein or generated hydrogen
atoms, but even if you didn't there is most likely some bad contacts
in the structure that will cause some atoms to have very high
potential energies when you start the simulation. This usually
causes the program to exit prematurely due to high velocities.
Minimization gets rid of all of these problems.


On Tuesday, June 15, 2004, at 01:25 PM, Xin Chen wrote:

> Hi,
> Do we need to do energy minimization for the pdb file before we use it
> to do
> simulation with NAMD? Thanks.
> Sincerely yours,
> Xin Chen
Michael Grabe, Ph.D.
Genetics Development & Behavioral Science Building
1550 4th Street, GD 481
San Francisco, CA 94143-0725
tel: ++ 415.476.0421

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