AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Tue Sep 16 2008 - 16:28:21 CDT

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
>> ============================================================
>> =======
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>>
>> ------------------------------
>> Novos endereços, o Yahoo! que você conhece. Crie um email novo<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.new.mail.yahoo.com/addresses>com a sua cara @
>> ymail.com ou @rocketmail.com.
>>
>
> 

-- 
Best wishes,

Myunggi Yi
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
myunggi_at_gmail.com

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu