Re: [AMBER] water cap simulation

From: <>
Date: Mon, 30 Apr 2012 19:48:49 +0000

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.


On , case <> 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
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