Internal PLUMED error:assertion failed i>0, serial of an atom cannot be zero

[guiden...@gmail.com]

When I use  GROMACS patched by plumed to simulation and use the keyword " MOLINFO", it kept telling me "Internal PLUMED error:assertion failed i>0, serial of an atom cannot be zero", and simulation was aborted. I don't know why? Here is my plumed.dat and error file.

[lapierr...@gmail.com]

Hi,

As the error message states, you should not have atom number 0 in your reference.pdb. If your atom numbering is starting from 0, try to renumber your atoms, if you have waters and ions in your pdb file making your atom number > 99999 and that you do not need them, just remove them from the reference (I had this problem once) and the final case I could think of is that you might have a big proteins with atom number > 99999 then try the hybrid 36 format as stated in the pdbreader plumed doc (https://www.plumed.org/doc-v2.5/user-doc/html/pdbreader.html).

Cheers,

Jeremy