VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 08 2013 - 12:47:05 CST

I would just start from the description of the text interface at
http://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/

I think something like this should just work:

pmepot -mol top -ewaldfactor 0.25 -grid 1.0 -pad 10 -loadmol top

Then he just has to add a volumetric representation.

Jim

On Fri, 8 Nov 2013, John Stone wrote:

> Any tips on how this person might automate PMEpot?
>
> Cheers,
> John
>
> ----- Forwarded message from Philippe Bopp <philippebopp_at_yahoo.com> -----
>
> Date: Wed, 6 Nov 2013 08:50:37 -0800 (PST)
> From: Philippe Bopp <philippebopp_at_yahoo.com>
> Subject: vmd-l: PME calculations
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
>
>
>
>
>
>  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)
> -----------------
>
> ----- End forwarded message -----
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>