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

[Mark Abraham]

Hi,

Depends which one... some of them extend the ensemble.

Mark

On Wed, Oct 4, 2017 at 5:36 PM Myunggi Yi <myunggi at pukyong.ac.kr> wrote:

> 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 <+82%2051-629-5773>
> Fax: +82 51 629 5779 <+82%2051-629-5779>
>
> 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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