[gmx-users] Restart Arbitrary Frame & Thermostat.

[Johnny Lu]

I ran gmxcheck on an old cpt file:

Command line:
  gmxcheck -f nve1.cpt

Checking file nve1.cpt
Precision mismatch for state entry box, code precision is float, file
precision is double
Precision mismatch for state entry x, code precision is float, file
precision is double
Precision mismatch for state entry v, code precision is float, file
precision is double

# Atoms  30360
Last frame         -1 time  838.960


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1


So, if a check point file is written at frame 1, and the first frame of the
whole simulation is frame 0, gmxcheck of the checkpoint file should give
last frame ... time 000.000 ? or 000.002, suppose the time step is 2 fs?



On Fri, Sep 19, 2014 at 1:43 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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