VMD-L Mailing List

From: Stephen Cox (stephen.cox.10_at_ucl.ac.uk)
Date: Sun Feb 06 2011 - 14:38:30 CST

Hi,

I am performing a Grand Canonical MC simulation, and due to the fluctuating
number of particles, I cannot load the trajectory as a single file. No
problem - I just adapted a script I saw on the mailing list and load each
frame individually:

foreach f [lsort [glob *.xyz]] {
    mol new $f type xyz waitfor all
}

However, it would be nice to change the graphical representations of all the
loaded frames, so that for example Carbon atoms (name C) are "VDW 1.000
23.000", Oxygens (name OW) are "VDW 0.800 23.00" and Hydrogens (name HW) are
"VDW 0.500 23.000". I tried adding something like

foreach f [lsort [glob *.xyz]] {
    mol new $f type xyz waitfor all
    mol modselect 0 0 name OW
    mol modstyle 0 0 VDW 0.800 23.000
    addrep 0
    .... ....
}

Which I took from logging the commands to a console, but it only works for
the first frame... I think I need to loop over the second "0" over all
molecules but I'm not too familiar with Tcl, so any help would be
appreciated.

Cheers,

Steve