Jason,
thanks for suggestions. Could you also tell me 1) may I use initial heating
of my system in NPT (not NVT) which could prevent such density fluctuations
during this stage using appropriate pressure coupling constant? 2) What
problems might be occurred during simulation in octahedral boxes?
James
2014-06-09 16:21 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Mon, 2014-06-09 at 12:17 +0400, James Starlight wrote:
> > Dear Amber users!
> >
> >
> > I've faced with the problems during equilibration of my protein using
> > pmemd.cuda
> >
> > 1- I've started to heat my protein in nvt and quickly obtained
> >
> > ERROR: Calculation halted. Periodic box dimensions have changed too much
> > from their initial values.
> > Your system density has likely changed by a large amount, probably from
> > starting the simulation from a structure a long way from equilibrium.
> >
> > [Although this error can also occur if the simulation has blown up for
> > some reason]
> >
> > The GPU code does not automatically reorganize grid cells and thus you
> > will need to restart the calculation from the previous restart file.
> > This will generate new grid cells and allow the calculation to
> continue.
> > It may be necessary to repeat this restarting multiple times if your
> > system
> > is a long way from an equilibrated density.
> >
> > Alternatively you can run with the CPU code until the density has
> > converged
> > and then switch back to the GPU code.
> >
> > visualization show me that individual water have been moved towards the
> box
> > boundaries being separated from the rest of the solvent.
> >
> > What would be best solution here
>
> Just restart the calculation using the latest restart file. pmemd.cuda
> will automatically divide up the system into cells based on the new
> volume, so the problem should go away.
>
> Once the volume and density have stabilized, you should not see this
> error again. (This is what the error message is telling you, and this
> error message is fairly descriptive as far as error messages go).
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Jun 09 2014 - 08:30:02 PDT
