[gmx-users] Error when performing MD with heavy atoms frozen

[Kai Hu]

Hi there,
I am new to GROMACS, went through Lysozeme in Water tutorial and everything
runs smoothly.
I then tried to immobilize all heavy atoms (except H) in md.mdp file by
specifying freezegrps               = Protein-H       ; Freeze all heavy
atoms
freezedim                = Y Y Y             ; Freeze all dimensions
towards the end of the file. I previous generated a index.ndx file using
gmx make_ndx command.

This time, a fatal error would show up, saying:
Fatal error:
Bond length not finite.

Can anyone tell me briefly what might be wrong that leads to such error?
Note, if I remove these two commands in md.mdp file, no error would pop up,
it seems something must wrong with the freeze commands.

Thanks in advance for any help!

--Kai

-- 
Kai Hu

Ph.D. candidate,
Allen's lab, W240-MSC
the Pennsylvania State University
+1-814-777-8651


*"When God closes a door, he always opens a window."*