[gmx-users] Restart Arbitrary Frame & Thermostat.

Fri Sep 19 21:42:40 CEST 2014

Just do it! ;-)

mdrun -nsteps 1

Mark

On Fri, Sep 19, 2014 at 9:29 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> I mean is the "last frame ... time", the time for the frame of the cpt
> file, or the frame right before the frame of the cpt file?
>
> On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > 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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