<t>I don't have a direct answer to your question, just a comment. I also outsourced only force computations to OpenMM from Molmodel. At first I had a lot of trouble figuring out what was going on because my CPU was 100% busy no matter what I did. I looked at it with Intel VTune and determined that i...

<t>Hi, Cho. A few things to try:<br/> (1) Comment out the loadPluginsFromDirectory() call at the beginning of the simulateArgon() fucntion. Then verify that you are able to run without the plugins (meaning you'll be using the Reference platform). If that works, then the problem is most likely troubl...

<t>Yeah, you're right! That's the same as before. <br/> <br/> Still, it is slightly more informative. That makes me think it isn't the cleanup of OpenMM objects (System, Integrator, Context) that's failing. Rather, it appears to be failing in the destructor for some global or static object that was ...

If you can run that one in gdb and get a stack trace it might be more informative than HelloArgon where the cleanup is being done inside anonymous destructor methods. We should be able to tell exactly what is being destroyed when disaster strikes.

<t>Hi, Sid. Do you also see this problem with the HelloSodiumChloride example? The reason I ask is that the HelloArgon example allocates the OpenMM System, Integrator, and Context on the stack and does no explicit cleanup while the NaCl one allocates them on the heap and cleans them up at the end. I...

Hi, Sid. I believe you just need multiple calls to PeriodicTorsionForce. Regards, Sherm

<t>Getting units right is surprisingly hard to do. In Sid's case he was very diligent about getting the units right in the hard cases yet missed one simple case. That's the kind of error that every human makes no matter how smart. It does seem kind of a shame that we have a nice C++ API but aren't t...

<r>(John Chodera posted this in thread "Units of force constants" -- I'm including it below to start a new thread.)<br/> <br/> BY: John Chodera (jchodera)<br/> DATE: 2009-07-04 23:25<br/> SUBJECT: RE: Units of force constants<br/> <br/> <br/> > I told you getting the units right is the hardest part!...

Let's start another thread for this discussion -- I think we wore this one out! I'll call it "Units conversion in OpenMM" and include your last post, John.

Sherm

That makes a lot of sense -- I assumed the positions you displayed were Angstroms, but if those were nm that was a very stretched water molecule!

Congratulations on finding that. I told you getting the units right is the hardest part!

Regards, Sherm