[gmx-users] Grompp checkpoint bug?

[Mark Abraham]

Hi,

I thought this was supposed to work (I wrote that doc sentence, but have
forgotten what's in the code). Can you please open an issue at
redmine.gromacs.org and attach suitable files so I can see how grompp is
working for you?

Thanks,

Mark

On Thu, Jul 9, 2015 at 8:06 AM Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:

> Hi everyone,
>
> I’m experiencing some discrepancies when I pass the checkpoint file to
> grompp using the -t checkpoint flag:
>
> grompp -f md.mdp -o md.tpr -p topol.top -c md_res_1.gro -t md_res_1.cpt
>
> This command results in a tpr file without any variables for barostat and
> thermostat:
> box (3x3):
>    box[    0]={ 6.70916e+00,  0.00000e+00,  0.00000e+00}
>    box[    1]={ 0.00000e+00,  6.70916e+00,  0.00000e+00}
>    box[    2]={ 3.35458e+00,  3.35458e+00,  4.74410e+00}
> box_rel (3x3):
>    box_rel[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    box_rel[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
>    box_rel[    2]={ 5.00000e-01,  5.00000e-01,  7.07108e-01}
> boxv (3x3):
>    boxv[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    boxv[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    boxv[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> pres_prev (3x3):
>    pres_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    pres_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    pres_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> svir_prev (3x3):
>    svir_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    svir_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    svir_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> fvir_prev (3x3):
>    fvir_prev[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    fvir_prev[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    fvir_prev[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> nosehoover_xi: not available
>
> These values are, however, present in the cpt file:
> box (3x3):
>    box[    0]={ 6.69977e+00,  0.00000e+00,  0.00000e+00}
>    box[    1]={ 0.00000e+00,  6.69977e+00,  0.00000e+00}
>    box[    2]={ 3.34989e+00,  3.34989e+00,  4.73746e+00}
> box-rel (3x3):
>    box-rel[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    box-rel[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
>    box-rel[    2]={ 5.00000e-01,  5.00000e-01,  7.07108e-01}
> box-v (3x3):
>    box-v[    0]={ 3.46479e-02,  0.00000e+00,  0.00000e+00}
>    box-v[    1]={ 0.00000e+00,  3.46479e-02,  0.00000e+00}
>    box-v[    2]={ 1.73240e-02,  1.73240e-02,  2.44998e-02}
> pres_prev (3x3):
>    pres_prev[    0]={ 5.48752e+02,  2.40244e+02, -2.50854e+02}
>    pres_prev[    1]={ 2.39676e+02, -8.38463e+01, -4.59079e+02}
>    pres_prev[    2]={-2.52490e+02, -4.60009e+02,  7.15652e-01}
> nosehoover-xi:   -0.265991    0.015571
>
> Running the tpr file and additionally providing the checkpoint through the
> ‘mdrun -cpi’ command produces a different output than running mdrun using
> the same tpr (even though the checkpoint has already been passed into
> grompp).
> This seems to be contrary to the intended behaviour, as the manual states:
> 'If you wish to change the ensemble or things like output frequency, then
> supplying the checkpoint file to gmx grompp with -t along with a new .mdp
> <http://manual.gromacs.org/online/mdp.html> file with -f is the
> recommended
> procedure.’
> If what I’m seeing is, in fact, the intended behaviour, it might be useful
> to explicitly mention the need to supplement grompp with the energy files
> as well in order to keep the barostat variables.
>
>
> Kind regards
>
> Dries
> --
> 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.