[gmx-users] Pbc and Com in simulation video

[Alan Dodd]

Yes, I know what you mean - I keep meaning to make a modified trjconv where '-fit trans' only affects the xy coordinates, for my bilayers, but it never quite seems important enough.  If your droplet moves at a constant rate, trjconv -shift will, I think, move the coordinates by an amount proportional to the framenumber (so at a constant speed) and then all you'd have to do is play with the periodicity. Never tried it though.
If you're making the movie with VMD (unpretty, but functional) you can control the periodic imagery quite well in a manner that may help.



----- Original Message ----
From: "janne.hirvi at joensuu.fi" <janne.hirvi at joensuu.fi>
To: gmx-users at gromacs.org
Sent: Tuesday, September 25, 2007 4:03:17 PM
Subject: [gmx-users] Pbc and Com in simulation video


Hello gmx-users!

I am trying to make a simulation video in which a water droplet is
rolling or sliding on a surface. Due to a periodic boundary conditions
a droplet is not whole all the time but it disappears from the right
and appears from the left in cycles.

I think that I could create more visual video by removing the lateral
motion of the center of mass of a droplet so that the droplet would
stay whole
in the middle of simulation window and the surface would translate
below the droplet. I am not exactly sure how realistic this kind of
video would be and would like to know if someone has better ideas?

If there are no better ideas I would need advices to be able to create
a such trajectory or video. Right now I am struggling with trjconv
which might be suitable for this purpose. However, if I use the
droplet as a group for translational fit (-fit translation) I get
trajectory in which the whole system wanders strangly (laterally (the
surface moves first to the left and then back to the right) and also
in perpendicular to the surface due to the lowering of the height of
the center of mass of the droplet during the simulation) and the
droplet wont stay whole in the middle of the box. Any ideas what I am
doing wrong or how I would be able to get rid of even this lateral
wandering so that I could at least see how realistic this procedure is?


Thanks for your time and help in advance,

Janne


------------------------------------------------------------------------------
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
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