Re: SMD Constant velocity pulling

From: jeevan gc (
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 <>

> 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?
> Thanks

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:20 CST