Please post to the mail list, not to me personally.
Missing atoms usually occur because your model is bad - e.g. atoms
move too far, too fast. If you’re not using good rRESPA params,
that can happen.
Steve
Dear Steve
I chosen respa parameters according to default values that there are in the manual for biomolecules, but I received the following error. Should I use this integrator for equilibration step as the producing step? Should I choose ‘morse’ bond_style that it includes stiffness parameter for applying stiff bonds?
Is there any other suggestion?
Regards
Nahid
Dear Steve
Which bond_style you suggest to have stiff spring bond?
Thanks alot
Regards
Nahid
What following error?
Steve
Bond atoms %d %d missing on proc %d at step %d
The SHAKE algorithm is incompatible with a small time step, because the algorithm tries to correct any deviations in a single step. When dt is small, the resulting corrections are large, and can cause the bond errors that you’re seeing.
However, it’s very hard for us to understand what you want to do—and why you’re having problems when you post things in a long series of posts, rather than a single post outlining what you’re trying to look at, what’s goi wrong, your scripts and input files, and so on.
–AEI