AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: julliane Yoneda (jullianeyoneda_at_yahoo.com.br)
Date: Wed Oct 01 2008 - 12:22:06 CDT

Dear Carlos,
 
Now I am using AMBER 9.
You told me to take care with ntb=0 and igb=0. What combination do you suggest me to use in a restrained simulation at vacuum?
Thank you very much;
                                             Julliane  

--- Em seg, 15/9/08, Carlos Simmerling <carlos.simmerling_at_gmail.com> escreveu:

De: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Assunto: Re: AMBER: Temperature regulation
Para: amber_at_scripps.edu
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.
carlos

On Mon, Sep 15, 2008 at 8:48 PM, julliane Yoneda
<jullianeyoneda_at_yahoo.com.br> 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
seems
> 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
because
> the temperature goes to 150K… I don't understand what is
happening…
> 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: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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