From: Athanassios Stavrakoudis (astavrak_at_cc.uoi.gr)
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,
Thanassis
> 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: http://stavrakoudis.econ.uoi.gr/
Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
GR-45110, Ioannina tel: +30 265 100 5935
GREECE fax: +30 265 100 5092
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