[gmx-users] pressure, pressure coupling, md-simulation

[Carsten Baldauf]

hi all//
I am running simulations of two peptides in a spc-water box. when i take 
a look on the pressur using g_energy i get a for me surprising result 
[see table attached at the end].
my paramters in the mdp-file:
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
i would have expected values that vary around 1, but not that strong ...
any comments?
thanks in advance//
carsten

time[ps]   pressure[bar]
    0.000000  758.267761
    0.500000  212.367020
    1.000000  120.587708
    1.500000  212.223999
    2.000000  165.683792
    2.500000  -29.302847
    3.000000  -153.361755
    3.500000  -139.225266
    4.000000   -5.481802
    4.500000   58.451248
    5.000000  -83.907234
    5.500000  -65.444496
    6.000000  -145.506271
    6.500000   82.083496
    7.000000  -44.367283
    7.500000   45.389313
    8.000000  -127.727112
    8.500000   20.940464
    9.000000  -88.312294
    9.500000   94.777344
   10.000000   31.043549
   10.500001  224.010498
   11.000001   20.522711
   11.500001   -6.741184
   12.000001  120.655266
   12.500001  -69.056061
   13.000001   24.855703
   13.500001  -124.957497
   14.000001  287.177277
   14.500001  255.671982
   15.000001  -68.855598
   15.500001   -3.723346
   16.000000  133.916824
   16.500000  165.818970
   17.000000  -40.751926
   17.500000  -31.959528
   18.000000   19.484137
   18.500000  201.772842
   19.000000  204.057877
   19.500000  -101.770378
   20.000000  155.598251
   20.500002  -16.176575
   21.000002  -367.913422
   21.500002  176.726685
   22.000002  204.842834
[...]
  560.500000  218.545822
  561.000000   45.322552
  561.500000   95.517212
  562.000000  -161.862534
  562.500000  -37.560928
  563.000000  164.321075
  563.500000    2.103663
  564.000000  188.659958
  564.500000  -120.343651
  565.000000  -60.852753
  565.500000  -69.009254
  566.000000  203.959213
  566.500000  -181.538834
  567.000000  -84.225761
  567.500000   75.202568
  568.000000   41.987900
  568.500000   86.207703
  569.000000  -98.482269
  569.500000  -46.558285
  570.000000  152.498047
  570.500000  119.676727
  571.000000  151.332291




-- 
dr carsten baldauf
biotechnologisches zentrum der tu dresden
http://www.biotec.tu-dresden.de/pisabarro
http://www.biotec.tu-dresden.de/~carstenb

Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

No Software Patents!
See http://www.ffii.org/index.en.html