RE: AMBER: sander bomb

From: Ross Walker <>
Date: Tue, 3 Apr 2007 08:35:40 -0700

Hi Janavi,
Take a look at your simulation in a visualization program such as VMD and
see if you can see what is happening. There are two likely possibilities for
what you are seeing.
The first is that your system is blowing up somehow. Perhaps one of the
inner shell waters is escaping through the outer shell and then boiling off
into space. This may be tricky to fix and you would likely be better trying
to setup a water cap. This applies restraints based on the distance and atom
is from the boundary rather than on specific atoms.
The second option is that your system picked up translational motion and has
translated a long way from the origin. This typically happens if you start
the simulation with a non-zero thermostat. It can also happen over time with
the Berendsen thermostat. Setting nscm typically fixes this but it is
possible that a value of 5000 is too high. Especially if the system starts
with a large amount of translational motion. Try running an initial 1000
step run with nscm=10. Then use the rst file from this as the restart
(irest=1,ntx=5) for your main run and then set nscm=1000. That way you get
rid of any initial translational motion quickly before starting your main
I hope that helps.
All the best
|\oss Walker

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From: [] On Behalf Of
janavi raghavan
Sent: Tuesday, April 03, 2007 07:29
Subject: AMBER: sander bomb

In my md run i am getting a sander bomb.the error is as follows:
Local SIZE OF NONBOND LIST = 1446256
 Frac coord min, max: 0.510295224658475 1.00159624388865
 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.
in one of the previous explanations about the sander bomb (dated:5/12/2005)
it was a periodic boundry system.i am using non-periodic boundary condition
with 2 shells of water with the outer shell being constrained by a large
harmonic potential.i am using nscm= 5000 ..........
could you please tell me the reason for this ocurrence and also how i could
rectify it.
thanking you in advance:


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Received on Wed Apr 04 2007 - 06:07:46 PDT
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