From: Benjamin Joseph Coscia (
Date: Thu Feb 02 2017 - 14:51:44 CST

Hello VMD users,

As stated, I have a strange error that occurs when trying to view a .gro
file for an initial configuration I wrote using a python script. When
trying to view it directly after running the script, VMD loads it and the
main window accurately displays the name of the molecule and the number of
atoms, however the display window is empty.

I am able to get around the problem by opening the .gro file, picking any
line in it, backspacing once, pressing the space bar (to reset it to the
way it was before), then saving and closing. When I open it again, the
molecule is displayed as expected!

I really don't know what would cause something like this. One thing that
may offer clues is that, in the past, I never ran into this issue using a
nearly identical script. The difference was that instead of writing a file
with the python script (using something along the lines of f.write() in the
script), I would use print statements and redirect the output from the
script to a file. For some reason that works.

I've attached the script I used if you want to recreate what I am seeing.
(note that it is a work in progress and is a mess, but works. The file
writing part is at the end).

If anyone has experienced this or has any ideas of what might be causing
this, I would appreciate any advice.


Benjamin Coscia
*Graduate Assistant -- Shirts Group*
*University of Colorado at Boulder*