AMBER Archive (2008)

Subject: Re: AMBER: Temperature regulation

From: julliane Yoneda (jullianeyoneda_at_yahoo.com.br)
Date: Wed Oct 08 2008 - 12:52:52 CDT

Thank you very much again Carlos!
It seems to be working now!
Best regards;
                                                  Julliane

--- 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, 23:04

yes, GB calculations need information that isn't in old prmtop files.
you should rebuild it in leap.

On Wed, Oct 1, 2008 at 9:10 PM, julliane Yoneda
<jullianeyoneda_at_yahoo.com.br> wrote:
> 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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