failure in RATTLE

From: Sangamesh B (forum.san_at_gmail.com)
Date: Tue Dec 16 2008 - 08:20:24 CST

Hello NAMD users,

I'm running NAMD-2.6 built with MPICH2 & GNU compilers on Rocks-5
Linux cluster. There were no errors during compilation.
The examples given with NAMD distribution were also working.

For one of the input file, the following error is appearing:

/opt/apps/namd26_gnu/Linux-amd64-MPI/charmrun +p4
/opt/apps/namd26_gnu/Linux-amd64-MPI/namd2 npt02.inp | tee
npt_result_out_ll
.
..

ERROR: Atom 3601 velocity is nan nan nan (limit is 10000)
ERROR: Atom 3602 velocity is nan nan nan (limit is 10000)
ERROR: Atom 3603 velocity is nan nan nan (limit is 10000)
ERROR: Atom 20926 velocity is nan nan nan (limit is 10000)
ERROR: Atom 20927 velocity is nan nan nan (limit is 10000)
ERROR: Atom 20928 velocity is nan nan nan (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 60!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 60!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 60!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 60!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 277!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 277!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 277!
ERROR: Constraint failure; simulation has become unstable.

..
ERROR: Atom 30757 velocity is nan nan nan (limit is 10000)
ERROR: Atom 30758 velocity is nan nan nan (limit is 10000)
ERROR: Atom 30759 velocity is nan nan nan (limit is 10000)
ERROR: Atom 34330 velocity is nan nan nan (limit is 10000)
ERROR: Atom 34331 velocity is nan nan nan (limit is 10000)
ERROR: Atom 34332 velocity is nan nan nan (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 480!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 480!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 480!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 480!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1082!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1082!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1082!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1082!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 703!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 703!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 4.136847 CPUTime: 4.136847 Memory: 128778 kB
End of program
ERROR: Exiting prematurely.
==========================================
WallClock: 4.144087 CPUTime: 4.144086 Memory: 128778 kB
End of program
ERROR: Constraint failure in RATTLE algorithm for atom 703!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 4.156466 CPUTime: 4.156467 Memory: 128778 kB
End of program
ERROR: Constraint failure in RATTLE algorithm for atom 703!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 4.164990 CPUTime: 4.164990 Memory: 128778 kB
End of program

I'm not understanding why these errors are appearing.

Are these errors due to wrong parameters in the input file or NAMD not
installed properly or else due to lower memory on the computer? (4 Gb
mem, run on single node)

Thanks in advance,
Sangamesh,
Consulatnt - HPC

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