From: Vermaas, Joshua (
Date: Mon Jul 30 2018 - 12:38:26 CDT

It is easy to track the public CVS, but quite a bit more difficult to contribute to it, and I think that is where the problem is. VMD has a number of longstanding issues that trip up new users, but that UIUC has not been able to dedicate resources to (such as using autoconf or cmake instead of the unconventional and easy-to-break configuration files now used to build VMD, or a library of scripts that can be user-contributed). Lets take the VMD build process as an example: it would be a pretty big change, but not one that an enterprising graduate student or CS undergrad or a bored/industrious postdoc couldn't handle. Right now, such a reorganization would be a massive pain to handle as John would need to deal with these edits by hand, make sure they don't break Windows builds, and go back and email the changer to see what's what, which makes it easy to lose track of things. Moving the CVS repository over to something a bit more modern like git means you've got relatively easy branch/merge features and travis making sure the builds don't break. Now lets consider the script library ( Right now, most of these are old (and very useful!) scripts Klaus's students have written over the years, since many folks just don't know that this resource exists without stumbling into it via google. Now imagine a "script examples" directory that would house this on github/bitbucket, so that these scripts and others found to be useful can just be uploaded without having to contact and waiting until a maintainer reads the email. Git just scales better when external contributors and collaborators are involved, and should definitely be the direction VMD goes in heading forward.


On 2018-07-30 08:34:30-06:00 wrote:

This is not a reply to the previous message, whose author didn't ask for one.

For other readers of the list, NAMD has a Gerrit portal:>

The code base of VMD still uses CVS, but this is easy to track it with a private Git repository, from which John integrates changes.

On Sun, Jul 29, 2018 at 3:19 PM Vlastimil ZÝma <<>> wrote:
Hi everybody,

as I'm finishing my PhD and heading out of world of molecular dynamics, I will most likely no longer use VMD.

I've tried several times to provide patches to VMD, but since it's so cumbersome, I'll put my effort into some other project. As I work as a programmer for several years now and also participate in open source projects I can only recommend to open the VMD source code to more developers. Using CVS and having patches send over email is a terrible approach when there are services such as GitHub, GitLab, BitBucket and others and modern version control systems.

All my molecular dynamics related projects are now open for new maintainers, as I most likely will no longer support them:
Well, all my projects at github are open for contributions, you can check any of those at>
Best wishes
Vlastimil ZÝma

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD>>