Re: Is it so different when setting reinitvels or not?

From: Jeff Comer (
Date: Wed Dec 17 2014 - 05:45:09 CST

The difference is that without reinitvels you are starting with a
temperature of zero. If you have a thermostat (langevin on, for
instance) it should pull the temperature up to desired after a few
thousand or so steps (depending on langevinDamping); however, it's
better to begin with a reasonable temperature.


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Dec 17, 2014 at 3:03 AM, Zhao Lina <> wrote:
> Dear all,
> In *.conf file, there are 2 commands for minimization as minimize and
> reinitvels. Then it can perform an equilibrium run. The commands looks
> like:
> minimize 1000 ;
> reinitvels $temperature ;
> run 50000 ; # 100ps
> But I found when reinitvels was commented or deleted as:
> minimize 1000 ;
> run 50000 ; # 100ps
> The equilibrium running still could be performed smoothly. Although,
> there is no reinitvels to redistribute the velocities for atoms, the
> velocities of the molecules and atoms in equilibrium run are not zero
> obviously. These atoms seems act with the normal random velocities
> according to the temperature set of *.conf file.
> So I'm wondering whether reinitvels is necessary before an equilibrium
> run? What's the real difference between setting reinitvels or not?
> Thanks a lot for your ideas!
> Lina

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