AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: julliane Yoneda (jullianeyoneda_at_yahoo.com.br)
Date: Wed Oct 01 2008 - 20:10:27 CDT

Thank you very much again...
But when I set igb=6 I have the following message:
"GB/PB calculations now require a new-style prmtop file"
The problem is that I created the prmtop file in AMBER 7??

--- Em qua, 1/10/08, 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: Quarta-feira, 1 de Outubro de 2008, 14:49

be careful of using a cutoff - you probably should not use one (make
it very large) unless you know that a cutoff is what you want. if you
use one, you might need to change the eedmeth option- check the manual
or the archives for details. also, you might try using the GB code to
do the nonperiodic calculation using igb=6, it may be more efficient
but you would want to compare both.

On Wed, Oct 1, 2008 at 1:22 PM, julliane Yoneda
<jullianeyoneda_at_yahoo.com.br> wrote:
> 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
>>
>> ________________________________
>> 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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