From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Oct 03 2013 - 09:06:37 CDT

Here are the instructions: http://www.ks.uiuc.edu/Research/vmd/alpha/

Regards,
Ajasja

On 3 October 2013 14:36, John Grime <jgrime_at_uchicago.edu> wrote:

> Thanks, Josh!
>
> I can't see a link to the 1.9.2 version of VMD on the official website
> (the latest precompiled binary seems to be 1.9.1) - I guess I'd need to
> apply for CVS access to download the source code and build VMD myself?
>
> Cheers,
>
> J.
>
> ------------------------------
> *From:* Josh Vermaas [vermaas2_at_illinois.edu]
> *Sent:* Wednesday, October 02, 2013 7:47 PM
> *To:* John Grime; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Creating very large solvation boxes
>
> 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.
>
>
>