[gmx-users] still change after equilibriated

[Yang Ye]

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
/