[gmx-users] Check point file

[Mark Abraham]

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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