Subject: Temperature Control in NAMD

From: Chen Hao <[email-masked]>
Date: Mon, 28 Oct 2002 18:43:00 +0800

Dear all:
    I used temperature coupling to control temperature in NAMD. But when 
I set temperature for heat bath to 298K, I found after 2000-3000 steps 
the termerature could stabilize to 298K(I set inital temp. to 298K, 
during the simulation temp. increased to about 318K quickly and then 
decreased to 298K slowly). what's the matter? If I used it to do a 
equilibrate simulation(system is temperature sensitive), would the first 
few thousand steps have any  influence?

Chen Hao

---

From: Jim Phillips <[email-masked]>
Date: Mon, 28 Oct 2002 13:53:13 -0600 (CST)

Hi,

This sounds like your system wasn't minimized at the beginning of the
simulation, and you are seeing the initial conversion of potential to
kinetic energy.  You should generally ignore the initial equilibration
period during analysis.

-Jim

On Mon, 28 Oct 2002, Chen Hao wrote:

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