VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Thu Feb 17 2005 - 11:52:30 CST

Nicolas,

what most likely happened is the following:
You used periodic boundary conditions in your simulation in combination
with the coordinate wrapping feature. That means whenever a water molecule
leaves the unit cell it is reinserted at the opposite site.
Both, the built in smoothing function and the smoothing script do their
job by calculating the arithmetic mean of the cartesian coordinates over
the specified time window. When a water molecules is wrapped around the
system boundaries it will consequenly appear in the middle of the box
after smoothing.

The solution is the following:
Do your simulation _without_ coordinate wrapping.
Then smooth your trajectory using trajectory_smooth.tcl.
After smoothing you can wrap the coordinates with pbcwrap.tcl from the
script library.

In case you don't want to repeat your simulations you can try to dewrap
them by identifying the wrapped molecules. There has been some traffic on
this list about that subject. I"m sure somebody has found a solution for
that. In principal you can modify the pbcwrap.tcl script to do the job.

Hope that helps,

Jan

> Dear VMD users,
> I have compute a trajectory in a box composed of 1 layer of dodecane
> surrounded by 2 layers of water. When I smooth the trajectory, some
> molecules of water appear in the middle of dodecane phase. I have used the
> "mol smoothrep" command line and the trajectory_smooth.tcl" script
> and they both have the same problem. Is there a problem with my trajectory
> or is it a bug?
>
> Thanks for your help!
>
>
> Nicolas Sapay
>
>
> _ Nicolas Sapay ________________________ PhD student _
>
>
> IBCP - Institut de Biologie et Chimie des Protéines
> Pôle BioInformatique Lyonnais - Gerland
>
>>> 7, Passage du Vercors
>>>
> 69367 Lyon cedex 07, France
>
>>> Tel : (33) (0)4 72 72 26 46
>>> Fax : (33) (0)4 72 72 26 04
>>>
>
> ____________________________________ n.sapay_at_ibcp.fr _
>
>