[gmx-users] about the position-restrained MD.

[Mark Abraham]

Liu Lin wrote:
> Dear gmx-users:
>  
>   I can not finish my position-restrained MD job. When the pr started 
> ,it stopped immediately. The log told that
> "Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 1108
> Fatal error:
> [ file "posre.itp", line 28 ]:
>              Atom index (27) in position_restraints out of bounds (1-25)"
> I can not find out the reason.

Your job didn't even start the MD... this error message says that grompp
is failing. Your position restraints file doesn't match your topology
somehow, but you'll have to work out why that is so.

Mark