MSMBuilder saves your trajectories in a fixed point representation, so it's warning you that the xyz coordinates are too big to be handled without errors. The most obvious cause of this would be if your XTC is not centered. Moving the center of mass to the origin would substantially reduce the magni...

Try setting the environment variable OMP_NUM_THREADS to 1?

Can you attach out the full stdout stream that comes from running `python setup.py build`. Also, for the call out to GCC that is actually throwing the link error, can you try executing that command by hand in the shell and then looking at what that prints to stderr. A segfaut on the tutorial is some...

If you use EPD python, it should just work, you don't have to do anything special This line: extra_link_args=['-L%s' % distutils.sysconfig.get_config_var('LIBDIR'),'-lpthread', '-lm', '-lgomp'] adds EPD Lib dir to the link line, which is where MKL shared object files are installed by default. I just...

Leo, One more question. Are you using a python distribution like EPD, the ubuntu system python, or one that you compiled from source yourself? The culprit here is that I think we're explicitly looking for MKL libraries in the place that they are installed with EPD python, the distribution that we re...

Leo, Thanks for your feedback. We're trying to make the installation process as smooth as possible, but there are definitely still some hiccups. In this case, it's basically just a bug in the setup.py file. If you're using MSMBuilder 2.5.1, open up the file setup.py in your favorite text editor, and...

Max, Sorry about this. One of the --source (-S) options is supposed to be file_dcd, which detects the DCD files, but this wasn't actually listed as a choice. I have a patch file for msmbuilder2.5 that fixes the problem, and in next release we'll have this fixed for good so that it just autodetects w...

Max, I'm glad that worked for you. Can you post the exception that you're getting from the ConvertDataToHDF.py? Which command line options are you passing? We made some improvements to the script in order to speed up the conversion, but there might be some holes in the test suite. If you can give me...

The easiest way to do this is to use MSMBuilder's Serializer object which wraps pytables. In msmbuilder2.5, you can get the object from an interactive python interpreter with "from msmbuilder import Serializer". In msmbuilder2.0, you can get the object with "from msmbuilder.Serializer import Seriali...

My guess is that you might be installing msmbuilder with a different version of python than what is being used by the scripts. When setting your path, can you put the /home/Max/Programs/epd-7.3.1-rh5-x86_64/bin before the rest of your path when resenting the path in your bash_profile, so that the EP...