Hi Brian, If you look near the middle of the ball, are the molecules overlapping (more precisely, do any intermolecular distances drop below 1.4 angstrom or so)? I'm curious about whether certain interaction terms are missing which would cause unphysical geometries to appear. Also, if you could prin...

In response to your posted issue, Robert just implemented some changes that improves compatibility with Python 2.6. It seems the argparse module is needed to get everything to work, which you pointed out can be installed using this command: pip install argparse Thanks for telling us about this, and ...

Hi Brian,

Your scripts look fine to me. How tight is the ball of solvent? Can you post a screenshot?

Thanks,

- Lee-Ping

Hi everyone, We'd like to announce the OpenMM command - a way for users to run an OpenMM simulation without writing a script. It is analogous to packages such as grompp/mdrun in GROMACS or tleap/pmemd in AMBER. A few features: - Sets up your system starting from coordinates and force field. - Config...

The answer is yes, but you actually need to be able to set up the simulation in TINKER. If you have custom molecules that aren't in the TINKER "params" directory, the correct way to do this is using a TINKER .key file (and optionally a .prm file). As long as you can run the simulation in TINKER, you...

Hi Karan, Thank you for asking your question. The functionality that you need is in the OpenMM - TINKER interface, which is available for download from the website. If you have already successfully compiled the OpenMM-accelerated TINKER software, it should automatically generate the System XML file ...

No problem, I'm glad the script worked! Still, it's very weird that VMD would not recognize such a simple function as "min". The bigger MM forces could be caused by using the LJ functional form, since it's too sharp in the repulsive region. You can try the Buckingham interaction as an alternative. T...

Hahahaha, I laughed out loud from that picture. :lol: There are two options for making this work: On line 82, I have no idea why the "min" command doesn't work, but it's not important and you can try replacing it with this expression: set radius [expr 0.1 * [veclength $vec]] On line 122, the "consta...

If you're not using Linux, one possibility is that different operating systems can use different characters to indicate the end of a line. Linux uses \n, whereas Mac OS uses \r and Windows uses \r\n. Can you open the script in a text editor, and look at the script with "cat", and let me know if anyt...

Hmm, that's very weird .. Are you running on Windows or Mac OS? I'm running on Linux.

In any case, the command "min" only appears on line 82 in my script. Try commenting out that line. You will get oversized arrowheads for tiny arrows, but it might work.