VMD-L Mailing List

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Mon Feb 25 2013 - 15:21:52 CST

The "coulombmsm" volmap with periodicity has some limitations, which is why it is not simply enabled through the GUI.

To enable it, you must define the environmental variable VMDMSMUSEPBC. (Its value shouldn't matter.)

Here are the limitations:
- the periodic cell must be orthogonal
- the volmap grid must fit within the cell (which can be a problem if you are attempting to average over a constant pressure simulation where the cell size is changing between frames)

Hope this helps.

-Dave

On Feb 25, 2013, at 3:03 PM, John Stone wrote:

> Hi,
> The "coulomb" volmap type doesn't support periodicity.
> The "coulombmsm" volmap type supports periodicity, but there are
> somewhat unusual cases that it currently can't handle, and this may
> be the reason that you're getting the error message. I'm CCing my
> colleague David Hardy, who developed the MSM (multilevel summation method)
> algorithm that is used by the "coulombmsm" volmap type, so he can
> comment further.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Feb 22, 2013 at 10:19:43AM -0500, Edward Lyman wrote:
>> Hi all,
>>
>> I found a very helpful post about running a volmap calc with pbc, from
>> last year:
>>
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/20684.html
>>
>> I can get the periodic version of the calc to start up, but I get the
>> 'illegal parameter' message mentioned at the bottom of the post. I tried
>> manually setting the grid for the calc to +/- 1/2 the box dimensions, but
>> I still get the error. If anyone can offer some input, I'd be grateful.
>>
>> Best,
>> Ed Lyman
>
> --
> 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/ Fax: 217-244-6078 

--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/