From: Jennifer Williams (Jennifer.Williams_at_ed.ac.uk)
Date: Tue Dec 08 2009 - 05:41:07 CST

Hello,

I am trying to look at a trajectory of my molecule. I have a long
alkyl chain anchored at one end. The problem arises because this chain
crosses over the periodic boundary conditions. I am visualizing a 2x2
cell as my unit cell is small.

I visualise the trajectory using dynamic bonds to prevent seeing long
bonds from one side to the other. The problem is not really the long
bonds but the missing ones. The bonds which cross the pbc appear
broken during those frames when one atom is on the other side of the
pbc-the bonds reform when both molecules are on the same side of the
pbc. So the trajectory looks strange as bonds are missing in one frame
and there in the next. I need all the bonds to appear in all of the
frames!

I have tried using the pbc join command but this appears to do nothing
to solve the problem. I used the following command

pbc join res -ref "name C2 C3"

which is accepted but the bonds do not join together. I think the
problem arises as I want to join one atom, C3, to a periodic image of
C2 in the next cell.

I have also tried using wrap and unwrap in various combinations with
join but I guess I am not giving the commands in the correct sequence
because nothing I do allows me to view a whole trajectory with
unbroken bonds.

Is there a way to save a 2x2x2 unit cell (and trajectory) as a 1x1x1
-so essentially VMD doesn't recognise the pbc which break up my
molecules? I only need to zoom in on one area so one complete alkyl
chain would be enough,

I'm using the lastest version of VMD 1.8.7. My trajectory comes from
gromacs (traj.xtc) so perhaps someone else has encountered this
problem and has a fix from within gromacs?

  Any help is much appreciated

  Jenny

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