From: Robin Betz (
Date: Thu Nov 22 2018 - 20:33:50 CST

Hi Guilherme,

Unfortunately getting VMD to run Python 3 as the built in interpreter
requires many changes in the source code, as there are significant changes
in the Python C API going from 2 to 3.
I've been working on adding this to VMD but it's taking some time as I'm
also making the Python interface easier to use by adding docstrings,
missing functionality, bugfixes, etc.

For now, you could install vmd-python as a standalone Python package from
conda forge if you're just wanting to do trajectory analysis and don't need
the GUI:
conda install -c conda-forge vmd-python

Hope this helps,

On Thu, Nov 22, 2018 at 6:19 PM Giacomo Fiorin <>

> Hello Guilherme, to use a Python version that is not ancient you need to
> build your own VMD, instead of using a pre-compiled build. This will also
> require manually editing the configure script, which has 2.5 hard-coded.
> See also:
> On Thu, Nov 22, 2018 at 2:53 PM Guilherme da Silva <>
> wrote:
>> Dear users,
>> Have anyone tried to use the python3 interpreter inside VMD? I was hoping
>> to use the numpy I have installed with Anaconda in order to do some
>> trajectory post-process.
>> I naively tried to play with PYTHONHOME and PYTHONPATH variables. The
>> gopython really recognizes the anaconda path, but keeps loading an
>> intrinsic 2.5 python version.
>> If nothing else, the only way to use numpy is to install an python2.5 in
>> order to install an appropriated version of numpy? I can mention the
>> alternative, but I was really
>> hoping some way to load the python3 or python2.7 libraries in the vmd
>> interpreter.
>> Thank you very much,
>> Guilherme
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD