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

[Myunggi Yi]

Peter,

(ignoring full precision) Are the thermostat and barostat computed by
coordinates and velocities, in principle ?


Myunggi Yi  (이명기, Ph. D.), Professor

Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of
Engineering
Interdisciplinary Program of Biomedical Mechanical & Electrical Engineering
Center for Marine-Integrated Biomedical Technology (BK21+)
College of Engineering
Pukyong National University (부경대학교 www.pknu.ac.kr)
45 Yongso-ro, Nam-gu (남구 용소로 45)
Busan, 48513, South Korea
Phone: +82 51 629 5773
Fax: +82 51 629 5779

On Wed, Oct 4, 2017 at 11:07 AM, Peter Kroon <p.c.kroon at rug.nl> wrote:

> Hi MY,
>
>
> actually you lose continuity of your simulation in both cases. The cpt
> file stores full precision coordinates and velocities (unlike gro/xtc).
> In addition, it stores state information about the simulation itself,
> such as the themostat and barostat. Whether this is an issue is up to
> you of course ;)
>
>
> Peter
>
>
> On 04-10-17 16:24, Myunggi Yi wrote:
> > 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
> >>>
> >>> ==================================================
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> >>
> >>
> >> --
> >> Regards,
> >> Tarak
> >> --
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