VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Oct 02 2013 - 19:47:40 CDT

Hi John,

There are two things I'd try:

Update VMD to the newest beta build for 1.9.2. There have been some
psfgen improvements, and I can't reproduce your problem now when trying
to build a 50 nm water cube (It took a long time, contained 12M atoms,
but it didn't break!), so I think whatever error you were getting may
have been fixed in newer builds.

If you can't/won't update VMD, you could give topotools a try. See the
documentation: http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
(you want the replicatemol feature).

-Josh

On 10/02/2013 04:45 PM, John Grime wrote:
>
> Hello all,
>
>
> I posted this message a couple of weeks ago, and there was no response
> at all, so I thought I'd repost it just in case it had fallen through
> the cracks and someone might see it and be able to help!
>
>
> I'm trying to generate very large solvation boxes in VMD (v 1.9.1 for
> Linux on AMD64), and I have some problems.
>
>
> Using the default segment prefix ("WT"), the solvation plugin runs
> until it tries to write the psf file, at which point it notices that
> the segid is longer than the 4 characters allowed in the PSF format
> and throws an error.
>
>
> Changing the segment prefix to "W" seems to fix this, but there are
> then problems with the PSF plugin in VMD which produce error messages
> like this:
>
>
> Info) Using plugin psf for structure file solvate.psf
>
> psfplugin) ERROR: Bond 8351722 references atom with index < 1!
>
> psfplugin) ERROR: skipping bond info due to bad atom indices
>
> ERROR) Error reading bond information.
>
>
> Is there a solution to this sort of issue? I'm trying to use the GUI
> version of VMD on a box with 64 GB of RAM, but if a command line
> solution exists then that's great!
>
>
> Regards,
>
>
> J.
>