VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Mon Feb 25 2013 - 15:20:43 CST

Hi all,

I developed a simple workaround:

-> round all box dimensions up to the nearest Angstrom. (for NPT
simulations, round up the largest observed box dimensions)
-> set the box dimensions to these values for all the frames
-> set the -res flag to 1.0 Ang
-> set the grid dimensions to match the rounded box dim and the res.

This is not perfect --- there is a little bit of vacuum around every
boundary. but it is simple and so far seems to give reasonable results.

If there is a more rigorous solution, I would be glad to have it!

E

On Mon, Feb 25, 2013 at 4:03 PM, John Stone <johns_at_ks.uiuc.edu> 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
>