[AMBER] Thanks , Ross!

From: song_jianing_hi <song_jianing_hi.126.com>
Date: Tue, 26 Jan 2010 14:16:16 +0800 (CST)

Hi Ross,

Thank you very much for your help.

You know, this is the first time I write to AMBER list .

I'm so worried whether there will be someone who will give me some advice and help me out of trouble.

You are so kind to give a detailed answer.

I'm so exited and enormously grateful for your help.

Thanks again!



2010-01-25 14:26:57"Ross Walker" <ross.rosswalker.co.uk> д
>Hi Song,
>You can use nmropt=1 to linearly scale the thermostat target temperature to
>your desired temperature. E.g.
> imin=0,irest=1,ntx=5,
> ...
> nstlim=1000000,dt=0.002,
> ...
> ntt=3, gamma_ln=2.0,
> ...
> nmropt=1,
>&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: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>AMBER mailing list

AMBER mailing list
Received on Mon Jan 25 2010 - 22:30:03 PST
Custom Search