[gmx-users] Pbc and Com in simulation video

[bmmothan at ucalgary.ca]

Hello Janne,

this is what I usually do when my molecules cross the box or dance all
around and it works for me:

I first do this with the "original" unmodified or fitted xtc or trr file:

trjconv -f  -o  -pbc nojump

then i take the modified trr or xtc and do a fit:

trjconv -f -s -fit rot+trans


Belquis


> 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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