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

[Mark Abraham]

A .cpt file has one frame in it. An .edr file has values and statistics
from many frames. Are you comparing things that are comparable?

Mark

On Wed, Dec 3, 2014 at 6:56 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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.
> >
> --
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