Constraint Failure in SMD simulation

From: Ramin Omidvar (
Date: Wed May 19 2010 - 11:51:20 CDT

Dear NAMD users,

Hi all,

I am running a SMD simulation to study the unfolding behavior of CNTN
protein based on tutorial's configuration file in "constant force pulling"
section but I have been faced with below error for 7 atoms (All atoms are
belong to CNTN molecule not to the solvent water molecules).

ERROR: Constraint failure in RATTLE algorithm for atom 4719!
ERROR: Constraint failure; simulation has become unstable.
ERROR: same as above for other six atoms

I played with TimeStep and decreased it several times and finally the
error was removed but I was forced to increase the number of steps and
total run time was not as enough as other usual simulations so I think that
it is not the most appropriate solution.

I would be so appreciated if somebody could show another way to me
or confirm my solution.

Any assistance is highly appreciated ,Thanks in advance,

Best regards
Ramin Omidvar
PhD student of Biomedical Engineering Dept.
AmirKabir University of Tech.

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