<t>I checked your numbers in Matlab and agree with you -- 0.000364 kcal/mol is the right answer. And I get that whether I work in Amber units or use your conversions to kJ/nm and back.<br/> <br/> So I think that narrows it down to the parts of the program we haven't seen. For example, the non-zero K...

<t>- for working out the bond terms I would suggest building your trivial example with no nonbonded forces at all, just to keep it simple<br/> - regarding 5-sided rings, all heavy atoms are 1-2 or 1-3 bonded along the shortest path, so NonbondedForce::createExceptionsFromBonds() will set all the non...

<t>Hi, Siddharth. HelloEthane is probably the best documentation at the moment and your last posted conversion looked correct to me. There was also a handout at the OpenMM Developer's Workshop giving all the OpenMM functional forms, but I don't know where to find an electronic copy of that.<br/> <br...

I must congratulate all us Molmodel developers on our restrained use of this forum!

Regards,
Sherm

A caution on OPLS: it uses a different Lennard-Jones mixing rule (Jorgensen's) than does OpenMM which currently supports only the Lorentz-Berthelot mixing rule used by Amber and Charmm.

Sherm

Thanks, Rob. I fixed up all the SimTK core CMake files to use the %ProgramFiles% environment variable (really "registry entry") so that will be in the next release.

I filed bug report #752 (now closed) so we can keep track of this fix.

Regards, Sherm

I see your point. Is there some reason it is desirable to have the clusters visible in the OpenMM API rather than buried as a platform? It is my (vague) understanding that OpenCL is following the cluster-is-just-a-platform path but it remains to be seen how that will work out.

Sherm

<t>This appears to have the problem that the same main program wouldn't work on a non-cluster system. The separate-platform idea could be used to shove the cluster down a level so that it would be invisible in user code.<br/> <br/> I'm thinking that one would want to develop the program, perhaps run...

<t>Thanks, J-O.<br/> <br/> Your code looks perfectly reasonable to me. It appears that the static symbol SimTK::Stage::HighestValid is not being found in SimTKcommon.lib where it should be. This is of course a very common symbol since it is used as the default value for the second realize() paramete...

Hi, J-O. Can you capture the link messages and post them? Thanks, Sherm