VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 22 2012 - 09:31:49 CDT

Hi,
  I'm happy to hear that you solved your problem already.
In regards to documenting the environment variables etc, the
issue is that the current MSM implementation in VMD can't handle
non-orthogonal PBC cells, so initially we put it in place with
the environment variable mechanism to allow it to be tested easily.
At this point I could probably expose the PBC MSM mode via the GUI
as it will either run or not run, for a given set of inputs, and the
code has enough error handling that it should report to the user why
it didn't run if it cannot for some reason. I'll look into this as
a possibility for the next VMD release.

We have a new MSM implementation in development that will ultimately
be faster and more flexible than the current code, but it probably
won't be ready to put into VMD until sometime early next year.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2012 at 02:40:24PM +0200, Bjørnar Jensen wrote:
> On 08/22/2012 01:19 PM, Bjo/rnar Jensen wrote:
>
> Nevertheless, the results appears to be for a non-periodic system, even
> though it states that
> it's running a periodic MSM calculation.
> I'm currently running VMD for LINUXAMD64, version 1.9.1 (February 1,
> 2012)
>
> So, the short and simple question:
> Is periodic calculation actually implemented or is it just running
> through the motions of a
> to-be-implemented function, and returning the results for a non-periodic
> calculation?
>
> Replying to my own original message:
> It turns out the calculation indeed is periodic. I accidentally executed
> the wrong script when
> visualizing it, thus displaying the data from a previous non-periodic
> calculation. My bad.
>
> The rest of my message is still valid, though. So thanks for the volmap
> tool, it certainly helps
> visualizing the effect of the electrostatic potential. A more
> user-friendly enable/disable pbc,
> along with the grid calculation would be helpful, though.
>
> Best Regards,
> Bjo/rnar Jensen 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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