[gmx-users] still change after equilibriated
Erik Lindahl
lindahl at sbc.su.se
Thu Dec 22 10:00:14 CET 2005
Hi,
That is NOT correct.
Pressure is a macroscopic property well-defined over 6*10^23 atoms or
so. The second you extrapolate this down to a couple of thousand
atoms you will observe very large fluctuations, which means you have
to run long simulations to get a good statistical average. This has
nothing to do with whether you are coupling the pressure or not.
The Berendsen algorithm does not result in a pure NPT ensemble, but
it is the only algorithm to _guarantee_ exponential relaxation to the
correct average pressure.
In this case the fluctuations are an order of magnitude higher than
the pressure difference, which probably means they are insignificant.
Cheers,
Erik
On Dec 22, 2005, at 8:46 AM, Yang Ye wrote:
> Despite possible simulation artifacts (protocol, solute, etc.), it is
> known that Gromacs' pressure coupling (at least Berendsen) could not
> give stable pressure. Check archive for similar topics.
>
> Yang Ye
>
> Rongliang Wu wrote:
>
>> Hello gmx-users,
>>
>> i have equilibriated a system after 7 ns, and out of curiosity i
>> continued run until 9ns. but i found the following phenomenon:
>> Statistics over 1000001 steps [ 5000.0000 thru 7000.0005
>> ps ], 9 data sets
>>
>> Energy Average RMSD Fluct.
>> Drift Tot-Drift
>> ---------------------------------------------------------------------
>> ----------
>> Potential -8174.09 0 0
>> -0.0167593 -33.5187
>> Temperature 299.735 0 0
>> -2.3866e-06 -0.0047732
>> Pressure (bar) 0.993253 417.974 417.974
>> -0.000471878 -0.943758
>> Box-X 3.27009 0 0
>> -7.43729e-07 -0.00148746
>> Density (SI) 967.094 0 0
>> 0.000662033 1.32407
>> Pres-XX (bar) 3.73019 721.395 719.606
>> -0.0879504 -175.901
>> Pres-YY (bar) 2.69262 624.848 623.924
>> -0.0588169 -117.634
>> Pres-ZZ (bar) -3.44305 728.557 723.708
>> 0.145352 290.704
>> #Surf*SurfTen -21.9101 2811.25 2780.78
>> 0.714987 1429.98
>> Heat Capacity Cv: 12.4718 J/mol K (factor = 0)
>>
>> Statistics over 1000001 steps [ 7000.0005 thru 9000.0000 ps ], 9
>> data sets
>>
>> Energy Average RMSD Fluct.
>> Drift Tot-Drift
>> ---------------------------------------------------------------------
>> ----------
>> Potential -8229.97 0 0
>> 0.0348891 69.7783
>> Temperature 299.735 0 0
>> 1.12632e-06 0.00225264
>> Pressure (bar) 1.10322 419.616 419.616
>> -0.000406983 -0.813967
>> Box-X 3.26972 0 0
>> 0 0
>> Density (SI) 967.428 0 0
>> 2.26927e-05 0.0453855
>> Pres-XX (bar) -57.2399 737.021 736.43
>> 0.0511137 102.227
>> Pres-YY (bar) 16.767 613.566 613.507
>> -0.0148347 -29.6693
>> Pres-ZZ (bar) 43.7826 732.279 731.959
>> -0.0375 -75
>> #Surf*SurfTen 209.332 2795.88 2793.91
>> -0.181749 -363.498
>> Heat Capacity Cv: 12.4718 J/mol K (factor = 0)
>>
>> why the pressure in different orientations becomes much larger. is
>> it that the only meaningful pressure value is the the scalar
>> pressure?
>>
>>
>> Thanks!
>>
>> Regards!
>>
>> Sincerely,
>>
>> Rongliang Wu
>> State Key Laboratory
>> of Polymer Physics and Chemistry
>> Center of Molecular Science
>> Institute of Chemistry
>> Chinese Academy of Sciences
>>
>>
>> wurl04 at iccas.ac.cn
>> 2005-12-20
>>
>>
>> ---------------------------------------------------------------------
>> ---
>>
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>
> --
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
>
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-----------------------------------------------------------
Erik Lindahl <lindahl at sbc.su.se> Backup address:
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91
Stockholm
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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