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.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.gmail.com>*escreveu:
>>
>> De: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Assunto: Re: AMBER: Temperature regulation
>> Para: amber.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.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.gmail.com
>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> ============================================================
>> =======
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.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.gmail.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Sep 17 2008 - 03:11:12 PDT
