RE: The problem of "SMD and smd.tcl"

From: Pijush Ghosh (
Date: Mon Jul 03 2006 - 22:43:57 CDT

Could you tell me what velocity and spring constant you are using? Try once
with decreasing the velocity and/or increasing the spring stiffness. I am
assuming you are using constant velocity method. May be you can attach the
configuration file you are using.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA

-----Original Message-----
From: [] On Behalf
Of James W
Sent: Monday, July 03, 2006 8:34 PM
Subject: namd-l: The problem of "SMD and smd.tcl"

Dear all ,
I used the SMD method to streching dimer , such as the deca-ala tutorial .
And the error is error1 . Could you tell me how to fix the problem ? thx

TCL: Running for 3000 steps
ERROR: Atom 2145 velocity is -444.451 -11508.2 -2272.15 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1882!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
WallClock: 1.325138 CPUTime: 1.240078 Memory: 29153 kB

National Center High-performance Computing (

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