[gmx-users] pressure coupling for lipid bilayer

[Nuno R. L. Ferreira]

On Thursday 02 May 2002 10:54 am, Shang-Te Danny Hsu wrote:
> 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

The off-diagonal values (3 last values) for tau_p, compressibility and ref_p, 
shouldn't be zero?

Nuno

>
> 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

-- 
**********************************************
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
Portugal
**********************************************