VMD-L Mailing List

From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Wed Aug 22 2012 - 06:19:08 CDT

Hello,
**
I've been trying to visualize the electrostatic potential within a
periodic crystal.

Initially when using the volmap tool it only ran non-periodic calculations.
By issuing the commands:

export MSMPOT_PBCON=1
export VMDMSMUSEPBC=1

in the linux shell prior to launching VMD I was able to run it with pbc:

**Info) Running periodic MSM calculation...

(This should be added to the documentation btw. I had to study the
source code
to figure out how to enable this, after reading an entry from John Stone
'hinting' that it
should be possible)

Nevertheless, the results appears to be for a non-periodic system, even
though it states that
it's running a periodic MSM calculation.
I'm currently running VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)

So, the short and simple question:
Is periodic calculation actually implemented or is it just running
through the motions of a
to-be-implemented function, and returning the results for a non-periodic
calculation?

NOTE:
Currently if the grid size (which is constructed based on the resolution
and apparently the
max/min xyz coordinates) happens to be smaller than the actual PBC, the
calculation will
not run. It returns error code 3 - Illegal Parameters.
I suggest that there should be an option to construct the grid based on
the periodic boundary
conditions rather than the max/min xyz as these does not always coincide.

Best Regards,
Bjørnar Jensen