[gmx-users] Pressure Fluctuations

[Kavyashree M]

Thank you Justin,

   When I went through most of the mailing list the fluctuations are not so
high
and even in the FAQ it was mentioned in the range of 500-600 bar for 216
water.
And more over the average pressure was ~6bar instead of 1bar which was
required.

  So would you suggest that I can proceed with this file for the production
run without
any problem. I was following your lysozyme tutorial where fluctuations were
much
less.. hence I suspected some problem in this data.

Thanking you
With regards
M. Kavyashree


On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Kavyashree M wrote:
>
>> Thank you Sir
>>
>>   I am using OPLSAA with tip4p water model, I agree to the fact that
>> it will oscillate but the oscillation is this case was from appr. -1000bar
>> to 1000bar. And as it is stated in the FAQ regarding the variation of
>> fluctuations with number of waters, this system has 6882 waters along
>> with a protein of 123 aa, so is not this fluctuations high?
>>
>
> No.  It is entirely expected, as you've been told.  Also pay attention to
> this statement from the page linked before:
>
> "How much it varies and the speed at which it does depends on the type of
> pressure coupling used and the value of the coupling constants."
>
> You may not see the exact same behavior described on the Pressure page if
> you're using different settings.
>
> There is no problem here.
>
> -Justin
>
>    Pressure coupling used -parinello-rahman
>>  tau_p = 2.0
>>  tau_t  = 1.0
>>  compressibility 4.5e-5
>>  Pcouple_type = isotropic
>>
>> Any suggestions?
>>
>> Thanking you
>> With Regards
>> M. Kavyashree
>>
>> On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham <mark.abraham at anu.edu.au<mailto:
>> mark.abraham at anu.edu.au>> wrote:
>>
>>
>>
>>    On 16/03/11, *Kavyashree M * <hmkvsri at gmail.com
>>    <mailto:hmkvsri at gmail.com>> wrote:
>>
>>>    Dear users,
>>>
>>>    Upon was trying to simulate an npt ensemble (protein in water),
>>>    pressure was coupled using  parinello rahman system with tau_p = 2,
>>>    tau_t = 1; compressibility 4.5e-5, type = isotropic.
>>>
>>>    (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
>>>    rcoulomb = 1.2; rlist = 1.2).
>>>
>>>    No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5),
>>>    the pressure
>>>    fluctuations are very drastic. I have gone through the mailing
>>>    list regarding
>>>    this issue but could not come to any conclusion.
>>>
>>>    Any suggestions are helpfull.
>>>
>>>    This is one of the statistics for pressure fluctuations.
>>>
>>>    Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 1
>>>    data sets
>>>    All statistics are over 100001 points
>>>
>>>    Energy                      Average   Err.Est.       RMSD  Tot-Drift
>>>
>>>  -------------------------------------------------------------------------------
>>>    Pressure                    5.77629       0.99    398.013
>>>  -5.34218  (bar)
>>>
>>
>>    Looks very normal. See http://www.gromacs.org/Documentation/FAQs
>>    number 3
>>
>>    Mark
>>    --
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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