AMBER: simulating a crystal using the unit cell

From: Sarah Wittkopp <>
Date: Thu, 14 Aug 2003 07:09:07 -0400 (EDT)


I am trying to simulate a crystal, where all atoms are not contained in
one unit cell. As a result, since the simulation is periodic I thought
the atoms outside of the box would be imaged in the other side. I think
the problem lies in that one cannot image all molecules in the unit cell.
I would like to know if it is possible to alter the imaging in sander
(AMBER 7) so it can be via atom rather than molecule, (which might be the

The NPT simulation does run when starting with a box size which contains
all molecules, and the structure has been checked.

I have tried starting with the crystal coordinates where some atoms
remained outside the box and recieved the following error.

 EWALD BOMB in subroutine ewald_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander

(Both PRESS, VIRIAL, and VDWAALS are way too large as well)

The same error was recieved when I tried two additional simulations, one
where the coordinates were imaged using ptraj by molecule and the other
was imaged by atom.

Thanks in advance for any help,

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Received on Thu Aug 14 2003 - 12:53:01 PDT
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