AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: julliane Yoneda (jullianeyoneda_at_yahoo.com.br)
Date: Tue Sep 16 2008 - 18:34:52 CDT

I restarted with the right previous MD restart files...
Thank you very much for your comments...

--- Em ter, 16/9/08, Myunggi Yi <myunggi_at_gmail.com> escreveu:

De: Myunggi Yi <myunggi_at_gmail.com>
Assunto: Re: AMBER: Temperature regulation
Para: amber_at_scripps.edu
Data: Terça-feira, 16 de Setembro de 2008, 18:28

Did you restart your simulations with the right previous MD restart files,
or same as the one used for the beginning of the simulation?

On Tue, Sep 16, 2008 at 2:22 PM, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

I have not used amber7 in many years, maybe someone else knows of issues in the old code. you should really upgrade, it's much faster, and I'm not sure anyone still tests or fixes Amber7 since it has been more than 6 years since it was released and the last amber7 bug fix was 3 years ago.

it does appear in your plot that the restarts are not done properly- have you applied all of the bug fixes?

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;
                                                           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
>
> ________________________________
> Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua
> cara @ymail.com ou @rocketmail.com. 

-- 
===================================================================
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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Best wishes,

Myunggi Yi
==================================
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Florida State University
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