AMBER Archive (2006)

Subject: Re: AMBER: AMBER : About the kinetic energy and temperature (GBSA model)

From: David A. Case (
Date: Tue Mar 28 2006 - 20:13:44 CST

On Wed, Mar 29, 2006, James W wrote:

> My system is SAMs (self assemble mileculars) , 120 units

It's not clear if you are simulation 1 unit (20 residues), or trying to
simulation 120 units (2400 residues). The latter would represent an enormous

> I am confused about the
> kinetic energy and temperature . I set the value of "temp0" equil to
> 300.0 k .But when " NSTEP " is 700 ,
> I found that "TEMP(K) = 3107.84" .

You have no temperature regulation, and started from what is probably
a non-equilibrated structure (since you set irest=0). You are not even
approximately conserving total energy, which may arise because of bad
forces in the system. Are you starting from a minimized structure? How
were the initial coordinates determined?

Be sure you have some experience with an "ordinary" protein or nucleic acid,
before embarking on a project where the initial structure might not be known
so well.


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