<r><br/> Hi Peter,<br/> <br/> I finally sorted this out. I wasn't calling my code with the flag for constraints, but there was a preference variable controlling the introduction of constraints that wasn't being initialized, hence the wonky behavior. Oddly, it never showed up until I was running usin...

Hmm ... so, now I ran the problem with constraints and can produce the error consistently. I will check on the other machine tomorrow to see if I somehow gave it the flag for constraints, and maybe I can sort it out next week at Stanford.

<t>I checked, and I define bond forces but not constraints. There are also nonbonded, angle and torsion forces defined. <br/> <br/> I can run the same set of examples, and half the time it gives the error, and the other half the time it runs. It also only seems to be occurring on one machine and onl...

<r>The error occurs immediately, but only some of the time. There are no constraints, so it cannot be #3. Perhaps #2 is the issue, except that I'm trying to run the minimization rather than dynamics. Clearly, expecting minimized input into a minimizer is problematic <E>:)</E> <br/> <br/> It also onl...

<t><br/> Sometimes I get this error when running using the reference platform, and sometimes everything works fine. I've traced it to the Shake algorithm within the reference platform files, but I have no idea what is going on. Sometimes everything works fine, and sometimes I get an error for every ...