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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 09 2014 - 05:30:04 PDT
