AMBER: periodic boundary condition question...

From: HL Eastwood <>
Date: Mon, 30 Oct 2006 14:42:53 +0000

Dear Amber guys

Is it possible to set up a periodic boundary simulation without putting
waters into it? I wish to examine how a helix aligns with it's own
dipole and I'd preferrably like a water-free box of 8 x 8 x 20
Angstroms to test it with. The AMBER manual refers only to a solvated
boxes, and when I create a box and delete waters and subsequently set
the job running I get the following error message:

SANDER BOMB in subroutine setup_grids
Resulting cutoff is too small for your lower limit

(This happens even when I set the non-bonded cutoffs to be 1).

My questions are therefore these:
1. How does one go about arbitrarily defining a box size?
2. Does a box in amber always have to correspond to those options
sepecified in xleap (ie. square or octahedral)
3. Is it in principal possible within the AMBER framework to run a
"solute only" perdiodic simulation?

Many thanks

Hayden Eastwood

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Received on Wed Nov 01 2006 - 06:07:13 PST
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