[gmx-users] Restart Arbitrary Frame & Thermostat.

[Mark Abraham]

On Fri, Sep 19, 2014 at 7:23 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Sorry for not being clear about the question.
>
> 1. If I start with NVT with thermostat A, and then continue with NPT with
> thermostat A, and barostat B, will the internal variables of thermostat A
> stays the same, upon transitioning from the NVT ensemble to NPT ensemble?
> 2. If I start with a NPT ensemble with thermostat A and barostat B with
> timestep 1 fs, and then continue with a NPT ensemble with thermostat A,
> barostat B, and timestep 0.5 fs, will the internal varaibles of thermostat
> A and barostat B stays the same?
>

Probably, but you can play with grompp with various combinations of -f
files and whether you give a checkpoint with -t and you can observe the
differences in the resulting .tpr files with gmx check -s1 -s2.

Mark


> Yes, the -cpnum will help a lot. Guess I will try that in next phase of the
> simulation. Thanks.
>
> On Fri, Sep 19, 2014 at 1:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On Fri, Sep 19, 2014 at 6:39 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> > > Hi.
> > >
> > > If I change ensemble (say, from NVT to NPT) but use the same
> > > thermostat/barostat, will the internal variables of the
> > thermostat/barostat
> > > stays the same (like how many step later to couple the system to
> > > thermostat)?
> > >
> >
> > I don't know what you're asking. nstpcouple and nsttcouple act
> > independently, though in practice there are restrictions.
> >
> > If I want to continue from a particular saved frame of the simulation
> > > (saved x,v,F, energy but not cpt file), and change the ensemble, is
> > grompp
> > > <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp> the
> only
> > > way to go?
> >
> >
> > If you haven't got a checkpoint for that time, then grompp is your only
> > friend for starting there.
> >
> > Can I make grompp to number the cpt files that it saves (like
> > > part0001.cpt, part0002.cpt...) ?
> > >
> >
> > grompp doesn't write checkpoint files. Do you want mdrun -cpnum?
> >
> > Mark
> >
> >
> > > Sorry for being nitpicky.
> > >
> > > Thanks again.
> > > --
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