While I've read the cautions in the User Manual about the half-step offset between the coordinates and velocities when using leap-frog based integrators when calculating energies, a point of confusion for me is how to properly handle restarting simulations. If I'm saving coordinates and velocities u...

Hi Peter,

Thanks for your reply. Is there a way on the OpenMM side to specify the OpenCL platform to use for a calculation? Is this just the OpenCLPlatformIndex property (I only found this digging around in the OpenMM Script Builder on Heroku)?

Josh

I'm starting to test out OpenMM using the python wrapper under OpenCL in the v5.1 beta release. My system has 4x Nvidia GTX 680s and a hexcore Intel CPU. I'm trying to understand how the device picking works when both are present and how device id's are assigned. I installed a nice little tool for e...

Before you follow my original advice to start digging through the source, I forgot that MSMB's command line tools are built around python's optparse module (I looked in the source since, when I answered you question, I was on a machine that I didn't have MSMB2 installed), so if you were to issue: Co...

Hi Max, Looking at the source code, ConvertDataToHDF.py has the ability to read .dcd files. I believe your problem however is that you are not supplying the 'source' argument to the script, and the default will only look for .xtc files. So I believe (without testing things however), that if you add:...

Hi Alex, I'm not one of the developers, but I've mucked around in the code a decent amount, so hopefully I can give you a bit of a hand. The sequence of states isn't going to be saved in the Trajectories directory. I believe that should only contain the concatenated trajectory files (raw data or pot...

In my original answer I suggested using HarmonicBondForce to restrain, instead of fix atoms. I made a mistake in that answer; you should use CustomExternalForce to restrain an atom to a position in space.

Josh  

<t>Hi Kasra,<br/> <br/> Since you're coming on and off of the GPU every integration step, you are paying a huge overhead which is killing the performance. This is not how OpenMM is intended to be used, so you can't really make a fair comparison to other software that has a built-in fixed atom functi...

<t>Zephyr is just running Gromacs, so I assume that you are getting either .trr or .xtc files for the outputs of your trajectories. If you take a look at the Zephyr User's Guide, there is an extensive section on pairing it with VMD, which is an excellent tool for visualizing molecular dynamics simul...

<t>Problem solved. The two GPUs had been switched into Exclusive compute mode, inadvertently, and changing them back to Default compute mode seems to have fixed things.<br/> <br/> The thing that I still don't understand, is that if I select the GPU device for each independent simulation and set the ...