[gmx-users] Different box volumes from gmxdump and g_energy

[Johnny Lu]

Hi.

I get two different volumes with g_energy and gmxdump.

Which one is true?

For now, I'm trying to get a NVT simulation with correct pressure, after a
300 ns NPT equilibration.
The 400 ns NPT equilibration has the following statistics, according to
g_energy of gromacs 4.6.7, and the equilibration seems to be sufficient.

      Last energy frame read 21438168 time 428763.375

      Statistics over 214381681 steps [ 0.0000 through 428763.3600 ps ], 5
data sets
      All statistics are over 17108015 points

      Energy                      Average   Err.Est.       RMSD  Tot-Drift

-------------------------------------------------------------------------------
      Total Energy                -307350        6.1        nan   -15.4944
(kJ/mol)
      Temperature                 299.851     0.0018        nan
-0.00756116  (K)
      Pressure                    1.01127    5.7e-05        nan
0.000126851  (bar)
      Volume                      298.385     0.0043        nan 0.00672558
(nm^3)
      Density                     1015.42      0.015        nan -0.0229017
(kg/m^3)

      gcq#328: "I used to be blond and stupid, but now I dyed it black"
(Miss Li)

      The nan in RMSD is caused by that I did one restart of the simulation.

Getting the correct volume is very important for me because the isothermal
compressibility of water is 4.5e-5, and a small change in volume can lead
to a relatively large change in pressure.

gromacs5.0.1. g_energy_d
      time(ps)         box-x       box-y       box-z     volume
      -------------    --------    --------    --------  ----------
      125142.100000    7.500611    7.500611    5.303739  298.383881

gromacs4.6.7. g_energy

      time(ps)       volume
      -------------  ----------
      125142.100000  298.383881

gromacs4.6.7. gmxdump
      box (3x3):
         box[    0]={ 7.50577e+00,  0.00000e+00,  0.00000e+00}
         box[    1]={ 0.00000e+00,  7.50577e+00,  0.00000e+00}
         box[    2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

      from the box vectors, volume is |z dot (x cross y)|
         7.50577 * 7.50577 * 5.30739 = 299.000218803

gromacs5.0.1. gmxdump_d
      box (3x3):
         box[    0]={ 7.50577e+00,  0.00000e+00,  0.00000e+00}
         box[    1]={ 0.00000e+00,  7.50577e+00,  0.00000e+00}
         box[    2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

example command for running gmx_dump:
      gmxdump_d -s ../npt13c.tpr -f ../npt13c_step62571050.cpt &>
gmxdump5.0.1d_step62571050

example command for running g_energy:
      g_energy_d -f ../npt13c.edr npt13c_volume_gromacs5.0.1_d.xvg

since the timestep is 0.002 ps, the time(ps) corresponding to
      the check point file is:

      62571050 * 0.002 = 125142.1 ps

All the files (tpr, cpt, edr) are generated by mdrun of gromacs4.6.7 (mixed
precision). It seems that it is ok to use the g_energy and gmxdump of
gromacs 5.0.1 on these files.

Size of the .edr file is 5 gb.

Thank you again.