[gmx-users] Pressure Fluctuations

[Justin A. Lemkul]

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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