We are attempting to constrain bonds on urea (an 8-atom molecule) using
SHAKE. The molecule has three bond types and we constrain them all with
fix 2 all shake 0.0001 20 0 b 1 3 2
When attempting to run the simulation, we keep receiving the error, "Shake
clusters are connected." The common error page defines the problem as "a
single cluster specified by the fix shake command must have a single central
atom with up to 3 other atoms bonded to it."
The molecule has three separate bond types and looks like the following:
H-N-C-N-H H 2 N 3 C 3 N 2 H
> > 2 2
H H H H
After playing with applying SHAKE to the bonds separately, it appears the
error only occurs when bonds 2 and 3 are involved in the fix. If we are
interpreting the error definition correctly, the problem is due to an
overlap between two competing central pairs (the two Ns) for the same
neighbor atom (C)? Is this situation not allowed, are we making a trivial
mistake or is this a bug?
The input and data file are attached.
Any help is very much appreciated. Thanks!
data.urea (2.5 KB)
in.urea (799 Bytes)