Hi Peter,

I've implemented the function to get permanent dipoles in the lab frame on both, the reference and CUDA platforms. I've checked the results manually against TINKER for a pure water box, and they match. Should I submit a pull request?

Thanks.
Saurabh

Hi Peter, I've forked and cloned the git repo, and am working on implementing the function. However, I was wondering how I should compile the code to test whatever I am coding up. The installation instructions in the user guide only outline the installations for the binaries, and I can't find any ob...

Hi Peter, I've found the function which returns the induced dipoles, and was able to use it. I was also wondering about the permanent dipoles in order to get the total dipole for each atom in the system. Lee-Ping mentioned in his last post on this thread that it would have to be implemented, and out...

Hi,

Has this function to get the permanent dipoles rotated in the lab frame been implemented?

Thanks.

Saurabh

Hi, I was facing this problem in October, and I wrote to CUDA. They initially replied saying that OSx 10.11 was not supported by any of their CUDA Tools versions, and then got back to me a few days later saying that they had only put up a new version of CUDA 7.5 which was compatible with OSx 10.11. ...

Thanks! This is definitely the way I should be going, instead of writing the whole system and then removing the waters. However, when I'm trying to set up the simulation as outlined in http://mdtraj.org/latest/examples/openmm.html , I am unable to use PME for the nonbondedMethod. It gives the follow...

Thanks for the code!

I could save these binary formats. However, I want to further analyze the trajectories that are generated using my own scripts. Is there any of these binary formats that could then easily be converted to PDB for processing after the simulation is completed?

Thank you.

Hi,

I'm simulating a solvated protein. Is there any way to configure PDBReporter to write the trajectory only for the protein atoms, and not write out the waters?

Thank you.

Hi Dr. Eastman,

I think I've been able to add the force I'm looking for using the global parameter update, as you've suggested.

Thank you.

Hi Dr. Eastman,

Has this feature been implemented? If not, if I use the global parameter, as you have suggested, is there a cost associated with setting the parameter at, say each time step?

Thank you.