[gmx-users] Wall option with 12-6 LJ

[Yutian Yang]

Dear all, 

I am trying to apply wall options using 12-6 LJ potential. Right now I am using isotropic  Berendsen pressure coupling, my first question is, is that the correct method? When I tried to use semi isotropic pressure coupling, the box dramatically expanded. And below is the simulation output: 

Statistics over 28078001 steps [ 100000.0000 through 240390.0000 ps ], 17 data sets
All statistics are over 5615601 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    1.00706     0.0044    15.9492 0.00507014  (bar)
Box-X                       31.9395     0.0022  0.0102715 0.00424252  (nm)
Box-Y                       10.6465    0.00074 0.00342382 0.00141418  (nm)
Box-Z                       10.6465    0.00074 0.00342382 0.00141418  (nm)
Density                     898.273       0.19   0.866606   -0.35772  (kg/m^3)
Pres-XX                    -29.6183       0.59    23.5225     2.3717  (bar)
Pres-XY                    0.214263      0.085    14.5115   0.105922  (bar)
Pres-XZ                  -2.36776e-05    0.00098    13.2336 -0.00170131  (bar)
Pres-YX                    0.214263      0.085    14.5115   0.105922  (bar)
Pres-YY                       -9.86       0.71    20.4194   0.168555  (bar)
Pres-YZ                  0.000270694    0.00072     13.379 -0.00244769  (bar)
Pres-ZX                  -2.45284e-05    0.00098    13.2336 -0.00170143  (bar)
Pres-ZY                  0.00027034    0.00072     13.379 -0.00244767  (bar)
Pres-ZZ                     42.4995       0.49     23.758   -2.52504  (bar)
LJ-SR:System-System         -774433        270    1020.16   -1115.05  (kJ/mol)
LJ-SR:System-wall0          8.65058      0.099    4.44415  -0.507431  (kJ/mol)
LJ-SR:System-wall1          8.65358        0.1    4.44156   -0.50994  (kJ/mol)

My question is, are the pressure tensors correct? Usually for an isotropic system, the diagonal terms should be around 1, but here they deviate a lot. 

Thank you! 


Sincerely
Yutian (Shirley) Yang
Biomedical and Chemical Engineering
329 Link Hall Syracuse University 
Syracuse NY 13244
yyang18 at syr.edu