From: Shultz, Jack (JShultz_at_nas.edu)
Date: Wed Sep 03 2008 - 20:13:24 CDT
Thanks for your help, I eventually got the Minimization and Equilibration and minimization on this membrane by recycling the parameter file used in tutorial 1-3-box. Among he changes I applied was
This made the simultion run much longer, but apparently all that minimization solved the RATTLE errors. If anyone is curious about the parameters I used, I can send the file. Thanks again.
From: owner-namd-l_at_ks.uiuc.edu on behalf of Shultz, Jack
Sent: Tue 9/2/2008 2:40 PM
To: NAMD list
Subject: namd-l: Constraint failure & velocity problem
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
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.
WallClock: 7.188000 CPUTime: 7.188000 Memory: 0 kB
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