[gmx-users] pressure coupling for lipid bilayer

[Shang-Te Danny Hsu]

This the result I obtain so far. The RMSD/fluctuation is always much 
larger than the mean value. I do monitor the changes of box dimension in 
all three axis. SO, should I wait until the box size is equilibrated?

==

POPC	72
SOL	2799	=> 38.9 SOL/POPC

Bilayer normal is along Y-axis

Pcoupl              =  Berendsen
Pcoupltype          =  Anisotropic
tau_p               =  2 2 2 2 2 2
compressibility     =  4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p               =  1.0 1.0 1.0 1.0 1.0 1.0

ref_T : 300K
============
Statistics over 94001 steps [ 0.0000 thru 188.0000 ps ], 9 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Pres-XX (bar)               28.2281    240.791     240.54  -0.202835   -38.1334
Pres-XY (bar)               4.46966    183.496     183.43   0.090342    16.9845
Pres-XZ (bar)               6.83516    157.098    156.237   0.302688    56.9059
Pres-YX (bar)               4.58106     183.48    183.445  0.0655349    12.3207
Pres-YY (bar)              -42.1243    334.214    333.365   0.438703     82.477
Pres-YZ (bar)              -4.88472     180.63    180.115  -0.250971    -47.183
Pres-ZX (bar)               6.83371    157.069    156.132   0.315729    59.3577
Pres-ZY (bar)              -5.15853    180.205    179.766  -0.231522   -43.5265
Pres-ZZ (bar)               27.7531     240.42    240.202  -0.188649   -35.4663

ref_T : 315K
============
Statistics over 95751 steps [ 0.0000 thru 191.5000 ps ], 9 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Pres-XX (bar)               33.5627    237.444    235.381  -0.564928   -108.185
Pres-XY (bar)               12.5019    185.515    185.494 -0.0507146   -9.71195
Pres-XZ (bar)              -14.6138    162.439    161.362  -0.337713   -64.6727
Pres-YX (bar)               12.7101    185.688    185.671 -0.0456346   -8.73912
Pres-YY (bar)              -41.0968    333.003    332.994  0.0450945    8.63569
Pres-YZ (bar)               8.87515    186.939     186.92 -0.0477162   -9.13774
Pres-ZX (bar)              -14.5316    162.497    161.295   -0.35696   -68.3586
Pres-ZY (bar)               8.83669     186.64    186.591 -0.0774553   -14.8328
Pres-ZZ (bar)               23.0678    245.781    243.334  -0.625814   -119.845



-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl