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

[Johnny Lu]

g_energy seems more correct than gmxdump in box size.


      [= npt13c_step169777880. 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}

      volume from box vector:
            7.50577 * 7.50577 * 5.30739 = 299.000218803

      [= npt13c. g_energy =]
      time(ps)       volume
      -------------  ----------
      339555.760000  298.385254

      [= commands for starting a NVT simulation, from the npt frame. =]
      ../../sofware/gromacs-4.6.7/bin/grompp -f nvt14d.mdp -c npt13c.tpr -t
npt13c_step169777880.cpt -o nvt14d.tpr

      [= gmxdump_nvt14d_step62571050. gmxdump =]
      box (3x3):
         box[    0]={ 7.50062e+00,  0.00000e+00,  0.00000e+00}
         box[    1]={ 0.00000e+00,  7.50062e+00,  0.00000e+00}
         box[    2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}

      volume from box vector:
            7.50062 * 7.50062 * 5.30375 = 298.385264414 (the same value in
g_energy of npt13c)

      [= gmxdump_nvt14d_step6247910. gmxdump =]
      box (3x3):
         box[    0]={ 7.50062e+00,  0.00000e+00,  0.00000e+00}
         box[    1]={ 0.00000e+00,  7.50062e+00,  0.00000e+00}
         box[    2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}

      volume from box vector:
            7.50062 * 7.50062 * 5.30375 = 298.385264414

On Wed, Dec 3, 2014 at 11:34 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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.
>