RE: [AMBER] trouble with cooling down the system

From: Ross Walker <>
Date: Sun, 24 Jan 2010 22:26:57 -0800

Hi Song,

You can use nmropt=1 to linearly scale the thermostat target temperature to
your desired temperature. E.g.

 ntt=3, gamma_ln=2.0,
&wt type='TEMP0', istep1=0, istep2=800000,
                   value1=800.0, value2=358.0 /
&wt type='TEMP0', istep1=800001, istep2=1000000,
                   value1=358.0, value2=358.0 /
&wt type='END' /

This will linearly scale the thermostat target temperature from 800K to 358K
between 0.0 and 1.6ns. Then for the last 400ps it will keep the thermostat
target temperature at 358K. You can create more complex profiles by use of
additional entries here. Also note that this changes the thermostat target
temperature and NOT the system temperature and so there will be a small lag
as the system slowly equilibrates towards the moving target temperature.

I hope this helps.

All the best

> -----Original Message-----
> From: [] On
> Behalf Of song_jianing_hi
> Sent: Saturday, January 23, 2010 2:04 AM
> To: amber
> Subject: [AMBER] trouble with cooling down the system
> Hello,
> When perform MD simulation using AMBER , I encounter the following
> problem.
> The system have been heated up to 800k ,and ,now ,I want to cool it
> down to 358k. What can I do? Can you give me some suggestion?
> One method I want to adopt is to reduce the temperture dramatically to
> 600K at the beginning , then ,cool it down to 358K. Is this OK?
> but I don't know time that needs for this cooling process.
> Thank you very much.
> I'm looking forward to your reply.
> Sincerely
> Nancy
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Received on Sun Jan 24 2010 - 22:30:03 PST
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