[gmx-users] Check point file

[Alex]

Hi Mark
Actually the simulation I am talking about is an annealing simulation in
which the system are being annealed from room temperature to 400 k during a
80 ns simulation and then the temperature are being ramped down again to be
at room temperature at 100 ns. Now I just want to keep continuing the
annealing from 80 ns (keeping the temperature at 400 k) instead of ramping
down. And If I start a completely brand new simulation the way you
mentioned, it does not continue the simulation at the annealed temperature
of my previous simulation.
I wish the state.cpt was also truncate-able likes the xtc and trr files to
have all at 80 ns.

Regards,
Alex

On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Mon., 24 Jun. 2019, 11:21 Alex, <alexanderwien2k at gmail.com> wrote:
>
> > Thanks Mark.
> > With not be able to append to the simulation files, you mean, I should
> not
> > use the "-cpi state.cpt" in the gmx mdrun, right?
>
>
> No, I mean you can't use -append. You have no relevant file for -cpi.
>
> > If
>
> > so, then, the
> > simulation is a completely brand new simulation excepts that it use -c
> > case.80ns.gro file as starting frame from t = 0.0. Then does the
> > trjcat/eneconv used for later concatenation know that the new outputs
> > should be assigned to the time t = 8000*1*?
> >
>
> The link I gave earlier has hints for how to prepare for this to go
> smoothly.
>
> In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything
> > are being continued from t = 100000.
> >
>
> Yes
>
> Mark
>
>
> > Thank you.
> > Alex
> >
> > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > No, that isn't meaningful. Follow
> > >
> > >
> >
> http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart
> > > but
> > > for the -c option, pass a file containing the desired frame extracted
> > from
> > > your .trr file. You will not be able to append to the simulation files,
> > but
> > > once the simulation is complete, you can concatenate all the files with
> > > trjcat/eneconv.
> > >
> > > Mark
> > >
> > > On Sun, 23 Jun 2019 at 22:53, Alex <alexanderwien2k at gmail.com> wrote:
> > >
> > > > Dear all,
> > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr,
> > > > case.100ns.cpt ... all are here,  I want to truncate the xtc file at
> 80
> > > ns
> > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr
> file.
> > > > Everything is clear for me except the case.cpt file for which is not
> > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr.
> > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,,
> > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point?
> > > >
> > > > Thank you.
> > > > Alex
> > > > --
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