From: Olaf Lenz (olenz_at_Physik.Uni-Bielefeld.DE)
Date: Fri Jul 16 2004 - 09:40:33 CDT

Hello once more!

I've written a simple file reader plugin to read data files of my coarse-grained
simulations. During this process, I came up with a few issues.

1. I provide the file reader plugin "olplugin" (that contains a plugin for the
file type "olmov") in my user directory. It is read in ".vmdrc" via a
"vmd_plugin_scandirectory" command (Is this command documented in the manual? I
have found it only on the mailing list.).

I can use it when loading a molecule interactively from the GUI. However, when I
try to use the plugin from the command line via

        vmd -olmov system.par

I get:
Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
Info) File loading in progress, please wait.
ERROR) Cannot read file of type olmov
ERROR) Loading of startup molecule files aborted.
Found 4 plugins or data handlers in directory

When I provide the plugin in the system plugin directory, the command works.
Apparently, ".vmdrc" is read after the file argument is evaluated.

2. To explain this, I need to give an example: I'm simulating a protein (i.e. a
cylinder in my case) in a lipid bilayer. We're using a constant pressure MC
simulation, that means that the system lengths fluctuate. The protein is placed
at a fixed position relative to the system length (like 0.5*L_x, 0.5*L_y).

I've written a structure file reader plugin that reads the structure of the
system from the simulation parameter file. Among other things, the file contains
the position of the protein relative to the system lengths.
A data file reader plugin reads the lipid positions from the simulation data
files for each timestep.
Unfortunately, now the data file reader plugin has no possibility to determine
the position of the protein, as this is given in the parameter file and not in
the simulation data.
As the system lengths changes in each timestep, the absolute position of the
protein changes, too, therefore I can't simply create one fixed cylinder for the
whole simulation.

To solve this problem it should be possible to somehow transport some data from
the structure file reader to the data file reader. Or is there another way?