AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: julliane Yoneda (
Date: Tue Sep 16 2008 - 13:05:27 CDT

Dear Carlos,
Thank you very much for your attention.
I am using AMBER 7. Thus, the restrained information is below the input I have sent you.
In fact there is no diference between average temperatures in the runs, but when I plot them (graphic attached) something seems to be strange.  May I trust in my results if the temperature oscillates like this?
Thank you very much again;

--- Em seg, 15/9/08, Carlos Simmerling <> escreveu:

De: Carlos Simmerling <>
Assunto: Re: AMBER: Temperature regulation
Data: Segunda-feira, 15 de Setembro de 2008, 22:07

I don't see anything that would obviously cause trouble in the
thermostat. using ntt=1 without setting the coupling constant may not
give tight control, though, depending on the default in your amber
version (see below).
ntr=1 won't work without additional info that you don't seem to have.
ntb=0 and igb=0 give you a combination that you need to think about
carefully, especially without anything in your &ewald namelist.
also- which amber version are you using? dtemp has been retired since
amber9 (see the manual).
is there a difference between average temperature in the previous run
and the current one? keep in mind that instantaneous T fluctuates, so
you need to look at averages.
maybe if you show us some of the output it will be more clear what's going

On Mon, Sep 15, 2008 at 8:48 PM, julliane Yoneda
<> wrote:
> Dear AMBER users,
> I am running a restrained molecular dynamics simulation in vacuum with the
> following input:
> &cntrl
> imin = 0, irest= 1, ntpr= 50, ntf=2,
> ntwx =100, ntb = 0, ntx = 5, ntc = 2, nsnb=10,
> nstlim = 100000, cut = 9.0, igb = 0, ntr=1,
> t = 30.0, dt =0.002,
> tempi = 300.0, temp0 = 300.0, ntt = 1, dtemp=4.,
> /
> &ewald
> /
> I divided the simulation in 10 parts using the same input. Everything
> to be ok in the output.
> The problem is that every time the simulation is restarted the temperature
> oscillates to 240 K… I tried to use ntt=4 but is seems to be worst
> the temperature goes to 150K… I don't understand what is
> Could someone help me, please?
> Thank you very much;
> Julliane Yoneda
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Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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