AMBER Archive (2006)

Subject: Re: AMBER: periodic boundary condition question...

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Mon Oct 30 2006 - 09:04:12 CST

Dear Mr. Eastwood,

yes, it is possible to create the periodic box using setBox command in
xleap and specifying the buffer.

setBox unit vdw Or centers {buffer ot buffer_xyz_list}

HL Eastwood wrote:
> 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?
With the buffer option.

> 2. Does a box in amber always have to correspond to those options
> sepecified in xleap (ie. square or octahedral)

As I found out (though I'm not sure) the only squareBox is available.

> 3. Is it in principal possible within the AMBER framework to run a
> "solute only" perdiodic simulation?
Yes.

Good Luck!

Sergey
>
>
> Many thanks
>
> Hayden Eastwood
>
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