Cool. May I ask which tool this is?

If I recall correctly, .top is not a fixed with format and there are no indentation issues, but there are many more places things could go wrong.

Hi Tobias, Thanks for pointing this out. I implemented the GRO file parser and there could be an issue with it, but in this case I think it's working properly. I think what's happening is that the residue number is usually right-indented while the residue name is usually left-indented so it looks li...

Great! Props for all of the good code and hard work!

I'm glad it's working now.

Hi Michael, It's good to hear that things might be working now. I understand it's a lot slower now but at least it's not running in double precision. :) Here's a quote from Jay Ponder discussing convergence criteria: >> A remaining decision is the level of convergence we should adopt as a >> standar...

Hi Kevin,

My experience has been that the Titan is quite a bit faster than the Keplers, and there have been no problems at all with simulation accuracy. Since the Titan is also cheaper, I personally think it's the way to go.

Thanks,

- Lee-Ping

Hi Martin,

Looking at your script, you set the properties dictionary, but I think you need to use it when creating the Simulation object. Something like:

simulation = Simulation(topology, system, integrator, platform, properties).

Thanks,

- Lee-Ping

Hi Michael, Thanks for your question. I can see a few things in your script that you can modify to troubleshoot the problem: 1) Try a time step of 0.5 fs. Due to the flexible bonds, a 1.0 fs simulation corresponds to artificial heating of about 10 degrees. 2) Try setting mutualInducedTargetEpsilon t...

Not sure - I'll ask Robert. I've always used argparse as a default.

Hi there,

We did get a CHARMM license just a few months back.

- Lee-Ping