RATTLE and DNA

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Tue Apr 05 2005 - 05:33:48 CDT

Dear All,

A student is doing a simulation of the Dickerson DNA dodecamer using the
scripts that I attach on this message (explicit waters, 22 sodium ions
placed with the program 'sodium'). The initial minimisation (down to a
'GRADIENT TOLERANCE: 1.0179') and heating stage appeared to go well. The
production run went smothly for ~0.7 nanoseconds, and then it died with

______________________________________________________________________

ERROR: Constraint failure in RATTLE algorithm for atom 364!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 146567.853583 CPUTime: 142235.640000 Memory: 16432 kB
______________________________________________________________________

He restarted his job, and this time he got to run it for another 1.3
nanoseconds before the problem re-appeared :

______________________________________________________________________

ERROR: Constraint failure in RATTLE algorithm for atom 375!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 255880.024668 CPUTime: 239782.650000 Memory: 14358 kB
______________________________________________________________________

He tried to switch off 'rigidDieOnError', but to no avail. The structure
(with the exception of the first base pair) appears to be fairly stable
(and the atoms mentioned above belong to the second base pair, not the
first). He is currently trying with a lower temperature (300K) [and if
that fails I suppose that we will have to either reduce the 2fs step, or
increase 'rigidTolerance'].

What buffles me, is that the simulation protocol he is using is fairly
standard (and can be found in numerous papers), so I didn't expect to have
these problems. Any suggestions would be greatly appreciated.

Regards,
Nicholas

-- 
            Dr Nicholas M. Glykos, Department of Molecular 
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
     Tel ++302551030620 (77620),  http://www.mbg.duth.gr/~glykos/


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