From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Sep 14 2011 - 00:31:59 CDT
The error is reported from "rigidbonds all" which also uses constraints, to
keep bonds with hydrogens rigid because the stretching effects can mostly be
ignored and save computing time (pls. correct me if I'm wrong), but that's
not the problem here I guess. Try running without rididbonds all (maybe with
only rigidbonds water), you should then get a different error message which
maybe points more to the really problem. Something like "Atoms moving to
fast". That would be a real indicator of bad initial structure.
As you already mentioned the two atoms reported are very close. You have
maybe not minimized long enough. I had a similar problem yesterday and
solved it by just minimizing a bit longer. You can check this easy with vmd
by plotting the energies of the minimization run in the output and look at
the end of the graph (be careful with the area of values for the Y-Axis
here, if you have really high peaks at the simulation start, the area will
be very huge and the smaller values at the minimization end will not be
showed, you will not see anything else then a constant line at the end of
the graph, you have to zoom it). If the area of fluctuation in total energy
is very small or even constant at the end, that's not the problem. If not,
and energy seems still decreasing, just minimize a little longer.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Jiao, Dian NMN (-EXP)
Gesendet: Dienstag, 13. September 2011 19:46
Betreff: namd-l: Constraint failure during equalibration
I built this system with an ion channel embedded in POPC lipid layer (just
followed the tutorial on setting up NAMD for membrane protein). Then I
started to equilibrate the system. According to the tutorial, I need to fix
the everything but the lipid tails to relax them at first. The conf file is
pretty much the same as the example file. After a while, the run stopped due
to the following error:
ERROR: Constraint failure in RATTLE algorithm for atom 14843!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
Atom 14843 is a lipid carbon. I can't tell what is wrong with that
particular atom by looking at the structure. I thought it must have to do
with the constraints, so I completely removed the constraints of lipids and
kept the protein fixed and ran minimization again. The job died again due to
the same type of error but different atom 14851. These two atoms are on the
same lipid and very close to each other. What is causing the problem? Is
that single lipid molecule that is messing up?
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