Well, for starters, did you change the compressibility value when you
run your simulations ? The default value in amber is for water, so you
need to change it in the input.
In any case, all solids and most liquids are incompressible as a general
rule.
Adrian
On 9/26/11 6:04 PM, Hernán Meier wrote:
>
> Dear Jason,
>
> Thanks for the prompt answer. We found this behaviour even in systems with extremely low water concentration. Could this happen because carbohydrates incompressibility is also very large?
>
> Regards,
>
> Hernán
>
>> Date: Thu, 22 Sep 2011 22:49:14 -0400
>> From: jason.swails.gmail.com
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] Large pressure fluctuations over the whole run
>>
>> Large pressure fluctuations are expected due to the fact that water is
>> largely incompressible. The metric you want to look at here is density if
>> you're looking for proper pressure equilibration, not so much pressure.
>>
>> HTH,
>> Jason
>>
>> On Thu, Sep 22, 2011 at 7:14 PM, Hernán Meier<hmeier.hotmail.com.ar> wrote:
>>
>>>
>>>
>>> Dear Amber users:
>>>
>>> We are doing MD calculations with Amber 11 and sander.mpi on a quaternary
>>> system (disaccharides + 1 amino-acid + water) with PBC in order to study
>>> transport properties.
>>>
>>> We did a 20.000 steps minimization combining Steepest Descent and Conjugate
>>> Gradient first keeping restrains and then 50.000 steps with the same combine
>>> methods without any restrain.
>>>
>>> After that we did a 50 ps constant volume MD with the same restrictions
>>> used during the minimization. Then we released the restrictions and followed
>>> the MD at constant pressure in several 500ps runs.
>>>
>>> We found that at the first run (of 500 ps) the average pressure lead to a
>>> high value. In the following runs this value rise fluctuating between 0.6 -
>>> 1.7 (the average) this value don't reach 1 even after 50 ns of running.
>>>
>>> Here are the inputs:
>>>
>>> Could anybody suggest us the possible reason for this behaviour, is it
>>> normal?
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> at NVT conditions:
>>>
>>> imin = 0,
>>> irest = 0,
>>> ntx = 1,
>>> ntb = 1,
>>> cut = 8,
>>> ntr = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 0.0,
>>> temp0 = 300,
>>> ntt = 3,
>>> gamma_ln = 2.0,
>>> nstlim = 25000, dt = 0.002,
>>> ntpr = 100, ntwx = 100, ntwr = 1000
>>>
>>> /
>>>
>>> 10.0
>>> RES 145 170
>>> END
>>> END
>>>
>>>
>>>
>>>
>>>
>>>
>>> at NTP conditions:
>>>
>>>
>>>
>>>
>>> imin = 0, irest = 1, ntx = 5,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 2.0,
>>> cut = 10, ntr = 0,
>>> ntc = 2, ntf = 2,
>>> tempi = 300.0, temp0 = 300.0,
>>> ntt = 3, ig = -1, gamma_ln = 2.0,
>>> nstlim = 250000, dt = 0.002,
>>> ntpr = 500, ntwx = 500, ntwr = 5000
>>>
>>> Waiting for a reply.
>>> Regards,
>>> Hernán Meier from Quitex Group UTN FRRe, Argentina
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Mon Sep 26 2011 - 15:30:03 PDT
