From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Wed Jul 27 2016 - 16:45:19 CDT
Your system is not equilibrated enough. SMD is an enhanced sampling method
which perturbs the system. Hence, pulling simulations we require a properly
equilibrated system. Also you could try with smaller time steps.
I think these errors and solution are already discussed in the namd thread.
On Wed, Jul 27, 2016 at 1:59 PM, Roshan Shrestha <roshanpra_at_gmail.com>
> Hello everyone,
> While running SMD constant velocity pulling of Ubiquitin, my simulation
> stopped abruptly with following error:
> Error: Constraint failure in RATTLE algorithm for atom 12261
> Error: Constraint failure ;simulation has become unstable
> Why these errors showed up and how to eliminate them?
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