Re: Constraint failure; simulation has become unstable

From: Athanassios Stavrakoudis (
Date: Fri Jan 07 2011 - 15:04:08 CST

Dear Wendy,

Multiple reasons may lead to this situation.
Most possibly, your system is not well minimized/equilibrated.
You need to give a more detailed description of your simulation
setup, to get more detailed answer.
Also search the NAMD-l archives, almost any user has come with this problem.

You can try to decrease the timestep to 1 fs,
or to decrease the nonbondedFreq, fullElectFrequency values.
Or to experiment with a mixture of all of these.

Good luck,
> Dear NAMD Users,
> I am working with 3 systems, the only difference between them are:
> a) 2 histidines protonated
> b) 1 histidine protonated, the second is neutral
> c) Both histidines neutral
> I run several nanoseconds of simulations on this systems and they did not
> have problems. I applied the reloadCharges command (increasing the charge of
> the same glutamate in the 3 systems) and the results are:
> a) Run normally
> b) ERROR: Constraint failure in RATTLE algorithm for atom XXXX ERROR:
> Constraint failure; simulation has become unstable.
> c) Run normally
> In case b) I said "atom XXXX", because I run 3 different simulations and the
> error is with a different atom each time.
> Any suggestion??? What could be happening???

Athanassios Stavrakoudis
University of Ioannina web:
Department of Economics e-mail:
GR-45110, Ioannina tel: +30 265 100 5935
GREECE fax: +30 265 100 5092

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