[gmx-users] Periodic saving of checkpoint file

[Mark Abraham]

Hi,

Looks OK. The details don't matter, as you are anyway changing ensemble.

Mark

On Thu, Nov 8, 2018 at 2:39 AM Nicolas Cheron <
nicolas.cheron.boulot at gmail.com> wrote:

> Hi Mark,
>
> Thank you for your answer. I didn't know this option. From what I have
> read, eneconv is for reading parameters for Nose-Hoover or
> Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation
> with the velocity-rescale thermostat or a Langevin dynamics, I don't need
> the .edr file, right ? Can you please confirm that this is enough to
> prepare the tpr from the time 50ps of the NVT simulation:
>
> gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr
> -time 50 -p Protein.top -po NVE_mdout.mdp
>
> Thank you
>
>
> Le lun. 5 nov. 2018 à 17:50, Mark Abraham <mark.j.abraham at gmail.com> a
> écrit :
>
> > Hi,
> >
> > Since you are anyway intending to change the ensemble, you can just use
> > nstxout, nstvout and nstenergy to write output every 10ps. That content
> is
> > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards
> to
> > split those up, and use them as inputs to grompp -e -t along with the
> > regular inputs.
> >
> > Mark
> >
> > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron <
> > nicolas.cheron.boulot at gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I would like to run a long NVT simulation and save a checkpoint file
> > every
> > > 10ps (in order to then run short NVE simulations from each checkpoint).
> > Is
> > > there a way to save a .cpt file every 10ps in an automatic way?
> > >
> > > I can do it with other program, for example with Amber "ntwr=-5000"
> will
> > > save a new restart file every 5000 steps. For now with Gromacs, the
> only
> > > thing I have found is to write a loop where at each step I extend the
> > > simulation time of 10ps with convert-tpr, perform the 10ps simulation,
> > save
> > > the .cpt, and then loop again.
> > >
> > > Thanks for your help.
> > >
> > > Nicolas
> > > --
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