Hi, I got a problem by simulating peptides and proteins with the Amoeba FF. If i start with a minimizied structure (density close to 1) and then heat my system up with a ramp the density decrease to a value of 0.7 and after a while reach a value of 0.95 to 0.98. I am quite sure that this density is ...

Hi Peter, Thanks for the quick response. I also tried CudaDeviceIndex but the same problem occured. I can set it to 20 and it is still running on the first gpu. I also tried to set device with OpenMM command. With the same result. So it seems that it is still ignoring this variable. Actually i found...

Hi, I have another problem running the OpenMM. I have two gpus in every machine and OpenMM was not able to decide which gpu is free and always tried to run the job on the first gpu. If a program already runs on the first gpu OpenMM is terminated. As i understood from the Python API i can force OpenM...

Hi again. Thanks for fixing the bug. I have another questions concerning simulations with amoeba and pbc. At the start of every simulation i got a lot of warning like this: /opt/rh/python27/root/usr/lib64/python2.7/site-packages/simtk/openmm/app/internal/pdbstructure.py:504: UserWarning: WARNING: du...

Thanks for your help so far. I am not sure what that third argument
std::vector<(Vec3,std::allocator<(Vec3)>)> dipoles
should be and how i define it.

Thanks for your help again.

Michael

That was exactly what i meant. Thanks for the quick response. I just tried to do what you suggested to print out the dipol vectors, but i am not sure if i am doing everything in a sensible way. Can you explain how i create a AmoebaMultipoleForce object in a sensible way. so what arguments i have to ...

Hi Peter,

Thanks for including that feature. Unfortunately i was quite busy this week, so i wasn't able to try.
I will try it as soon as possible.
But a second question occured this week. Is it possible to add a charge plasma or a background charge grid to a OpenMM simulation?

Michael

Hi Peter,

I am using the binary distribution.
if i am using the command
Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
the Amoeba Cuda package is loaded.

Hi Peter,

If you can provide some details on that for me, it would be great and i give it a go.

Thanks

Hi,

I just started using OpenMM and would need some help by setting up easy things.
Can you tell me how i can set up a reporter who is writing my the induced dipol moments(Amoeba) of an atom every x steps?

Thanks,

Michael