VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Thu Feb 17 2005 - 13:59:19 CST

Hi Nicolas,

Apparently, some of the water molecules cross the limit of the periodic box,
and they are wrapped to the other side in the next frame. To smooth the
trajectories, VMD interpolates coordinates between successive frames, thus
creating an artificial situation where water appears in the middle of the
dodecane phase.

The simple solutions I can see are either not to use trajectory smoothing for
water, or not to wrap water coordinates back into the unit cell. If you only
have data with wrapped coordinates, it should be possible to 'unwrap' them.

Cheers,
Jerome

Le jeudi 17 Février 2005 17:06, Nicolas Sapay a écrit :
> 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 _ 

-- 
Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 71
http://www.edam.uhp-nancy.fr/