OpenCLDeviceIndex refers to the index into the list of devices: i in your code. The numeric value of a cl_device_id has no meaning. Just think of them as opaque handles.

Peter

It sounds like that isn't the problem then. To debug this, I suggest creating a minimal test case with just a few atoms and an energy function for which you know the correct result in advance. For example, arrange four atoms to form a particular angle, then set your energy expression equal to angle1...

To parallelize across multiple GPUs I would explicitly have to call setDeviceIndex([0,1]) or the equivalent? Correct. So would the CPU be device ID 3? That depends on the OpenCL implementation. Nvidia's version of OpenCL doesn't support running on the CPU at all. On the other hand, AMD's and Intel'...

I don't have much experience with AmberTools myself. Anyone with more experience want to comment?

Peter

If a function is actually returning nan then multiplying it by 0 may not work. The result could still come out nan. But as long as it has a well defined finite value, this should work correctly. Perhaps roundoff error is causing the arguments to go outside the allowed range? Try replacing "acos(x)" ...

Hi Siddharth, The logic for automatically picking a device is entirely based on the properties of the device. It has no idea what else is running on a particular device at the same time. So if you start two simulations and let each one pick the device automatically, both of them will pick the same d...

Hi Siddharth, The logic for automatically picking a device is entirely based on the properties of the device. It has no idea what else is running on a particular device at the same time. So if you start two simulations and let each one pick the device automatically, both of them will pick the same d...

Hi Siddharth, The logic for automatically picking a device is entirely based on the properties of the device. It has no idea what else is running on a particular device at the same time. So if you start two simulations and let each one pick the device automatically, both of them will pick the same d...

Hi Ian,

The simplest thing will be to just build the whole model with AmberTools, water included.

Peter

Hi Ian, Right now, OpenMM doesn't include a tool to generate force field parameters for arbitrary organic molecules. The built in force fields just provide parameters for the standard amino acids, nucleotides, etc. So I suggest using AmberTools to prepare your system. You can use antechamber to gene...