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

From: wang (
Date: Mon Jul 03 2006 - 22:58:24 CDT

Dear all ,
I fixed my problem . I think the distance of two atoms is too closed
and let's the velocity too large .
After I minimized the initial structure and used the minimized
structure , the problem is fixed .


>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
> 701-231-6491(Lab)
> 701-231-4341(Res)
>-----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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