Dr. Case,
Thank you very much. The problem I encountered was:
" RE_POSITION Moving by -0.732505 -1.738350 -0.759695
Frac coord min, max: 5.043972078567463E-002 1.00022436972064
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error"
And I did use non-periodic boundary and constant NVT for my simulation.
Then I had the above problem.
Could you provide any suggestions? Thank you very much.
Yi
On , case <case.biomaps.rutgers.edu> wrote:
> On Fri, Apr 27, 2012, Yi An wrote:
> >
> > I'm trying to simulate a protein in a water cap. My problem is during
> the
> > equilibration and simulation stages, water molecules come out of the
> cap so
> > the simulation stops.
> It would help to have a better description of the symptoms of the failure.
> Can you describe what you mean by "water molecules come out of the cap"?
> Are
> there any messages when the simulation stops?
> > Looks like I have to use non-periodic boundary water
> > caps and I can't use constant pressure ensembles. Is this the reason why
> > waters drift out?
> This is confusing: water caps can only be used for non-periodic
> simulations.
> It doesn't make sense to have a water cap in a periodic simulation. Is
> that
> what you are trying to do?
> ...dac
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Received on Mon Apr 30 2012 - 13:00:03 PDT
