Date: Mon Mar 06 2006 - 09:23:09 CST

Maybe, too obvious but... about a bigger water box in the simulation? So the peptide won't move
to the border walls of the box, or is the peptide too big?

Another suggestion would be to fix one atom (as close as possible from the
center of mass) in the simulation in order to null the translation effect
(without affecting the rotation of the protein) to the walls.


Date: Mon, 6 Mar 2006 01:06:50 +0100
From: "L. Michel Espinoza-Fonseca" <>
Subject: vmd-l: pbc and vmd

Dear all,

I've been trying to analyze the contacts between water and a given
peptide from my trajectories. I used a nice script provided by one of
the VMD users. Everything went well, except from the fact that VMD is
not able to count the water molecules around my peptide from the image
of my periodic box. I've read some issues related to the pbc and VMD
(computation of hbonds, for instance), and according to what I read,
there is not such handling of pbc in VMD. Do you have any suggestions?
I tried to use some artifacts such as drawing images of the water box,
but it didn't work.



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