Hi Jason,
Thanks for your reply. The error is :
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.
Regards
Kshatresh
On Wed, Feb 11, 2015 at 2:05 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Feb 11, 2015 at 6:36 AM, Kshatresh Dutta Dubey <
> kshatresh.gmail.com>
> wrote:
>
> > Hi,
> >
> > I am using amber 14 GPU code for my simulation. Simulation crashes during
> > the NPT equilibration with error periodic box dimension too large.
>
>
> ​What is the exact error message? Is it that the *changes* in the periodic
> box dimensions are too large? Or that the dimensions themselves are too
> large? Or that the cutoff is too large (i.e., the box has shrunk too much
> for your cutoff+skinnb)?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 11 2015 - 04:30:03 PST
