VMD-L Mailing List

From: Philippe Bopp (philippebopp_at_yahoo.com)
Date: Wed Nov 06 2013 - 10:50:37 CST

 dear all

 I am trying to use the VMD-PME tool to analyze field fluctuations
 (in space & time).

 If I run it via the gui, it seems to work (even though I am not
 quite sure what it does, but hta can be looked up).

I log to file what I do
 - load a few frames

 - set the charges via the Tk console
 - use the Analysis->PME electrostatics gui
   reduce the resolution to 100x100x100
   give a file name
   click off the create new volume slice

  the log file looks like this (blank lines and omissions are mine)

# VMD for LINUXAMD64, version 1.9 (March 14, 2011)
# Log file '/home/pbopp/gabconfigs/quest.log', created by user pbopp
menu files off
menu files on

animate style Loop

display resetview

mol addrep 0
display resetview

mol new {/home/pbopp/gabconfigs/NR-10-1/KS.N.xyz} type {xyz} first 0 last 4 step 1 waitfor 1
animate style Loop
menu files off
menu tkcon off
menu tkcon on
menu tkcon off
menu pmepot off
menu pmepot on

animate style Loop
display resetview
mol representation Isosurface
mol addrep 1

mol new {/var/tmp/pmedx_q8baXWZY10} type {dx} first 0 last -1 step 1 waitfor -1

animate style Loop
mol rename 1 {KS.N.xyz PME}
mol delrep 0 1
menu pmepot off
mol off 0
menu graphics off
menu graphics on
mol color Name
mol representation Isosurface 0.500000 0 2 2 1 1
mol selection all
mol material Opaque
mol addrep 1
display projection Orthographic

10 zillions of   rotate x by 0.666667
.
.
.
rotate y by 0.133333

mol modstyle 1 1 VolumeSlice 0.510000 0.000000 0.000000 2.000000
.
a further zillion of such instructions
.
mol modstyle 1 1 VolumeSlice 1.000000 0.000000 0.000000 2.000000
# VMD for LINUXAMD64, version 1.9 (March 14, 2011)
# end of log file.

I thought I would just modify it, put it in a loop, write the stuff to
as many files as I have frames, but I havn't managed because I simply do not
understand what happens.

Where is pmepot
http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/
called?

Where are my parameters (e.g. the resolution)?
If I load this file (or -e it on the command line)
it works (sometimes, sometimes not, I can't tell,
may be depending on what I did before)
but sometimes! So the information must be there

somewhere.

Where do i screw up?

cheers & thanks

Philippe

-----------------
Philippe A. Bopp

Philippe.Bopp AT u-bordeaux1.fr   (office)
philippebopp  AT yahoo.com       (private)
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