Re: Constraint failure & velocity problem

From: bo liu (
Date: Wed Sep 03 2008 - 00:08:15 CDT

Hi Jack,

This means that the atom is too far from its reference position. not
necessarily relates to poor minimization.
i suggest you check the reference pdb and the initial coordinate file in
NAMD simulation,
if the constrained atom is too far from its reference position, you would
like to modify the coordinates of that atom in VMD or check whether the
reference position is reasonable.

hope it helps

2008/9/3 Peter Freddolino <>

> Hi Jack,
> this usually means that either you haven't minimized long enough, or you're
> using too long a timestep (or something along those lines that makes your
> system unstable). Constraining the atoms whose motion is becoming unstable
> is *not* a good solution to this. How have you set up your system?
> Best,
> Peter
> Shultz, Jack wrote:
>> I was getting a bunch of Constraint failures, then I got most of them to
>> disappear by setting the beta to 1 in the constraint and fixed atom file
>> for all the problem atoms. I still get a constraint failure for one of
>> them. I also don't know why I get this velocity error. Changing the
>> temperature has no effect. Any ideas?
>> TCL: Running for 250000 steps
>> ERROR: Constraint failure in RATTLE algorithm for atom 2482!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Atom 1207 velocity is 1.00258e+007 -1.17511e+007 -9.39458e+006
>> (limit is
>> 10000)
>> ERROR: Atoms moving too fast; simulation has become unstable.
>> ERROR: Exiting prematurely.
>> ==========================================
>> WallClock: 7.188000 CPUTime: 7.188000 Memory: 0 kB
>> Program finished.

-Liu bo
Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
Chinese Academy of Sciences, Beijing P.R. China
Office: (86)-010-88233187
Home: (86)-010-88259765
Cell: 13426057875

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