[gmx-users] Pres-XX and Pres-YY difference

[Johnny Lu]

I also ran another NPT simulation with Berendsen barostat, after those 300
ns of NPT with Parrinello-Rahman barostat. So the two simulations in these
two emails have the same starting point.
This simulation uses 2 fs time step, while the one above use 1 fs time step.

Below is the pressure tensor extracted with g_energy of mixed precision
gromacs 4.6.7.

Last energy frame read 236353 time 47270.602

Statistics over 23635301 steps [ 0.0000 through 47270.6000 ps ], 9 data sets
All statistics are over 236354 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pres-XX                     1.00041       0.72    212.365    1.26091  (bar)
Pres-XY                  -0.0733808       0.39    138.148   -1.94821  (bar)
Pres-XZ                  -0.0559881       0.23    138.047   0.135325  (bar)
Pres-YX                  -0.0785166       0.39    138.148   -1.99506  (bar)
Pres-YY                     1.52045       0.42     212.52     0.2362  (bar)
Pres-YZ                    0.142665        0.6    137.845     -1.995  (bar)
Pres-ZX                  -0.0616126       0.23    138.045   0.141702  (bar)
Pres-ZY                    0.135693        0.6    137.843   -1.95285  (bar)
Pres-ZZ                    0.821679       0.59    212.735    3.79446  (bar)


The shear part of the pressure tensor is smaller. But the normal part
(XX,YY, and ZZ) are still different.

The XX part of the pressure tensor in both simulations are very close to 1
bar, the target pressure, while the YY and ZZ part are not as close to 1
bar.

On Fri, Oct 10, 2014 at 10:03 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi. The following seems a bit strange to me. It was extracted from the edr
> file with g_energy of mixed precision gromacs 4.6.7.
>
> Statistics over 31921501 steps [ 0.0000 through 31921.5000 ps ], 9 data
> sets
> All statistics are over 319216 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Pres-XX                     1.00863       0.23    222.874 0.00505598  (bar)
> Pres-XY                   -0.218743       0.33    138.143    2.17256  (bar)
> Pres-XZ                   -0.233072       0.33    137.629    1.36597  (bar)
> Pres-YX                   -0.262129       0.32    138.137    2.12662  (bar)
> Pres-YY                    0.788658       0.23     225.34   0.928867  (bar)
> Pres-YZ                  -0.0207522       0.23    138.913    1.08012  (bar)
> Pres-ZX                   -0.276173       0.33    137.619    1.40069  (bar)
> Pres-ZY                   -0.098337       0.23    138.913    1.14865  (bar)
> Pres-ZZ                     0.60576       0.38    222.687  -0.259413  (bar)
>
> I don't know the meaning of Pres-XX. But I guess it means the pressure at
> some direction (some kind of tensor.).
>
> Why the pressure at XX direction is different from other direction?
> I thought Pres-XX should be same as Pres-YY and Pres-ZZ.
>
> The box is a truncated dodecahedron, the barostat was set to 1 bar, and
> the simulation was ran with mixed precision gromacs 4.6.7 with Parrinello-Rahman
> barostat for NPT simulation of about 300 ns before this stretch of NPT
> simulation.
>
> Thank you again.
>