VMD-L Mailing List

From: Dan Lussier (dtlussier_at_gmail.com)
Date: Fri Apr 17 2009 - 09:05:06 CDT

I had tried to send this message through a couple of days ago but it
never got posted to the list. I had an attachment on the email which
I'm guessing was responsible for it not getting through.

---------------------

I am trying to use VMD to visualize the output from a LAMMPS
simulation with periodic boundary conditions. When trying to
visualize the system I first load the psf file defining the system and
then the dcd file output from LAMMPS. The simulation is essentially a
slab of water and the problem I am running into is that some of the
bonds btw water molecule atoms are long in CPK or bonds
representation. (I can send an image of what I'm seeing off the list
if necessary.) In reading through the VMD documentation this issue
appears to be somewhat normal for simulation results with PBC.

To 'correct' the problem I am looking to use the pbctools suite on the
alpha version of 1.8.7 on Linux (32-bit). What I would like to do is
to wrap the coordinates into the nearest image and then fix the
elongated bonds problem. In looking at the pbctools documentation I
thought of trying:

pbc join res -ref "chain W"
pbc wrap -all

In trying this series of commands I don't get very far though as the
pbc join ... command causes VMD to crash (terminate called after
throwing an instance of 'std::bad_alloc' what(): St9bad_alloc).

At this point I'm not sure where the problem lies because I'm not sure
that my instructions to the pbc join command are ok as I wasn't sure
how to interpret the instructions for identifying the 'compound' in
the pbc join command.

I recognize that this issue is pretty diffuse at this point but if
anyone could give some advice, or a couple more examples, on how best
to use the pbc tool, particularly pbc join that would be great and
would help in isolating the problem.

Dan