Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon Jan 29 2007 - 15:04:22 CST

Hi Won-Young,
By specifying "wrapWater on" in your NAMD configuration file, NAMD
will wrap the coordinates of water molecules. "wrapAll" and
"wrapNearest" provide similar functionality.

 From the NAMD User's Guide (http://www.ks.uiuc.edu/Research/namd/
current/ug/) under "Periodic boundary conditions":
# wrapWater < wrap water coordinates around periodic boundaries? >
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally output relative to the way they
were read in. Hence, if part of a molecule crosses a periodic
boundary it is not translated to the other side of the cell on
output. This option alters this behavior for water molecules only.

# wrapAll < wrap all coordinates around periodic boundaries? >
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally output relative to the way they
were read in. Hence, if part of a molecule crosses a periodic
boundary it is not translated to the other side of the cell on
output. This option alters this behavior for all contiguous clusters
of bonded atoms.

# wrapNearest < use nearest image to cell origin when wrapping
coordinates? >
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally wrapped to the diagonal unit
cell centered on the origin. This option, combined with wrapWater or
wrapAll, wraps coordinates to the nearest image to the origin,
providing hexagonal or other cell shapes.

-Tim

On Jan 29, 2007, at 1:42 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:

> Dear NAMD users,
>
> I ran a molecular dynamic simulation in a NVT ensemble with NAMD.
>
> When I tried to examine the trajectory with VMD, I noticed that
> some water molecules are located outside of the periodic box. Is
> that possible? If it is possible, how can I wrap all water
> molecules in a periodic box.
>
> Thanks,
>
> Won-Young
>
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