From: John Grime (
Date: Thu Oct 03 2013 - 07:36:44 CDT

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?



From: Josh Vermaas []
Sent: Wednesday, October 02, 2013 7:47 PM
To: John Grime;
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: (you want the replicatemol feature).


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!