Hi Lee-Ping, Thanks for taking the time to look at my data. I've looked attached total energy and temperature graphs below, and there doesn't look like much is changing there. I've also attached a screenshot in the middle of the water ball and have set the H-bond distance to 1.4A. As you can see the...

Here's a screenshot of Frame 1 and frame 100. The water ball re-expands at the end of the simulation.
Frame 1 Frame 100

I recently ran a 50 ns explicit water simulation and had the waters and ions collapse into a tight ball in the center of the box for some unknown reason. Some waters remained associated with my protein, but <99% dropped into this cluster. At the end of the simulation the water ball started expanding...

Peter, I installed a Nvidia GTX 780 and I am no longer having these issues. I ran a 50ns implicit simulation with no errors and am currently running a 10ns explicit simulation where everything looks to be going well. I think the GPU was either overheating or the memory was failing. Thanks for your h...

Hi Peter, I've been having this problem for the last month when trying to run simulations, and I haven't been able to run past ~1.5ns on any simulation. I've attached the scripts below I use to set up the system and to run the simulation below. Both were derived from the user guide. Another possible...

I recently upgraded to OpenMM 5.1 and am running it on my Windows 7 PC with a Nvidia GTX 580. I have been running implicit solvent simulations (amber99sb) of a 265 amino acid protein using a script modified from the OpenMM script builder (OpenCL or CUDA, single precision). I can start the simulation...

Hi Joy,

Serves me right for not reading the instruction manual... ;') Are there any plans on having a repository for extended OpenMM forcefields or ligand/solvent parameters in the xml format since it's different than is used by other programs?

Best,

-Brian

I am interested in adding phosphorylated residues (serines/threonines/tyrosines) and other ligands (GTP/SAH) (http://www.pharmacy.manchester.ac.uk/bryce/amber) to my simulations in OpenMM. Is there a guide or instructions for updating the .xml force field files OpenMM uses to add new parameters? I'v...

Is there a similar fix for Zephyr running on Linux (ubuntu 11.04, 32 bit)? I installed Zephyr on a Windows XP machine a while back and replacing the Cuda 4.0 .dll files with the Cuda 3.1 .dll files did the trick. I recently installed Cuda 4.0 on a new Linux box and am getting the same reverting to r...

Thanks Mark. I had installed the CUDA 3.2, so I uninstalled that version and installed the 3.1 toolkit. Worked like a charm.