Re: Constraint Failure in SMD simulation

Date: Wed May 19 2010 - 14:48:31 CDT


That error means that indeed your system is crashing due to the perturbation you are applying. As you noticed short time steps do the trick, Maybe the energy function for your system is too sharp and you'll need to pay that price. Anyways, decreasing the applied force also could solve your problem. Of course supposing that you system is well equilibrated, otherwise it will always crash.

----Mensaje original----


Fecha: 19-05-2010 12:51

Para: <>

Asunto: namd-l: Constraint Failure in SMD simulation

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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