[gmx-users] continue simulation from intermediate frame instead of last frame

[Myunggi Yi]

1. In principle, MD can be restarted if there are coordinates and
velocities on the snapshot.

2. Even if you don't have velocity, you can assign random velocity with the
specific temperature.
In this case, you lose continuity of simulation. Don't worry.
If you run same simulation with the exactly same inputs (including the same
random seed), you won't get exactly same trajectory in most cases
(depending on simulation types and hardware, etc).

MY


On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar <tarak20489 at gmail.com> wrote:

> In that case, I think I do not have any option. The gmx_mpi_d check has
> only the last frame. :(
>
> Command line:
>   gmx_mpi_d check -f ../state.cpt
>
> Checking file ../state.cpt
>
> # Atoms  10703
> Last frame         -1 time 190772.080
>
>
> Item        #frames Timestep (ps)
> Step             1
> Time             1
> Lambda           1
> Coords           1
> Velocities       1
> Forces           0
> Box              1
>
> Thanks for your replies. I appreciate it.
>
>
> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 10/4/17 9:06 AM, tarak karmakar wrote:
> >
> >> Hi Justin,
> >> Thanks for the quick reply.
> >>
> >> Is there any way to check if the frame is there in .cpt file or not?
> >>
> >> I did the following exercise at difference 'time=' values,
> >> gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time
> >> 40000 -o topol.tpr
> >>
> >> It seems in all the cases, the trajectory gets restarted from the last
> >> frame.
> >>
> >>
> > The .cpt files are always overwritten unless you tell mdrun to keep them.
> > You can inspect the contents of any given .cpt file with gmx check.
> >
> > -Justin
> >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> > --
> > 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.
> >
>
>
>
> --
> Regards,
> Tarak
> --
> 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.
>