From: John Stone (
Date: Mon Jul 30 2018 - 11:56:46 CDT

Just FYI,
  Our experience with git on the NAMD side has not been without issues.
In fact, we have had as much or more difficulity training people to use
Gerrit than we ever had with having people send us diffs via email.
The fact is that working on large scientific software is hard work,
and one is either prepared to do that work, or not. Whether the code
is in git, mercurial, svn, cvs, or whatever, hardly makes any practical
difference. I've used them all and most of the issues come down to the
quality of the code contributions if/when they occur, and the diligence
of the contributor in testing their code. I would say that something like
99% of my time is spent on the latter issue. If someone can't deal with
diffs, then they may not be willing to properly test their code either.

The revision control system in use is probably the least important aspect
of software development at this level. Our experience with NAMD and Gerritt
is causing things to move in a new direction there, and when we have
come to what we think is a better solution on the NAMD side, we'll see about
moving VMD to match. So far the git/Gerrit attempt over the past year+
has not been a panacea. Several of the key NAMD contributors were completely
blown away by the complexity of working with the code review system, and this
ended up creating more problems for us than it has solved thus far. Until
things are working well with git on the NAMD side, I don't expect to change
anything on the VMD side, it would be wasted effort until we feel that
there's a net positive outcome.


On Mon, Jul 30, 2018 at 12:33:01PM -0400, Ivan Gregoretti wrote:
> Hi Giacomo.
> I think that migrating to Git is a good idea. It feels like the right
> thing to do in 2018.
> Git might be more attractive than CVS to the younger generation of
> users and contributors.
> I am thinking of student interns as an example. Blessed be all of
> them. They have great ideas and they speak Git nowadays.
> What do people think?
> Thank you.
> Ivan
> PS: VMD is jealous because only NAMD got a Gerrit privilege. :)
> ######################################################
> On Mon, Jul 30, 2018 at 9:40 AM, Giacomo Fiorin
> <> 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
> >
> >

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349