[gmx-users] Different box volumes from gmxdump and g_energy
Johnny Lu
johnny.lu128 at gmail.com
Wed Dec 3 19:08:25 CET 2014
yes.
I get an xvg file from the edr file with g_energy. Then from the xvg file,
i selected the observable (volume) corresponding to the timestep at which
the .cpt file is written.
Then I compared this value of volume, with the value of volume calculated
from the box vectors in the .cpt file.
On Wed, Dec 3, 2014 at 1:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list