Re: No effect of periodic boundary conditions?

From: Peter Freddolino (
Date: Wed May 23 2007 - 09:24:21 CDT

Hi Philipp,
the coordinates written to the dcd are only wrapped around the periodic
box if you turn on wrapAll or wrapWater. The effects of the boundary
conditions are present even if the coordinates are not wrapped, though.

Philipp Schoen1 wrote:
> Dear NAMD users,
> I have a rectangular box with water and a slab of solid material in the
> center. If I run a sequence of time frames in VMD I see that the water box
> remains stable but the slab moves on the lateral direction OUT of the
> periodic box?
> Do I miss something?
> Thanks
> Philipp

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