AW: fixed atom/Constraint failure in RATTLE algorithm/

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jun 03 2013 - 00:23:43 CDT

Hi Mehran,

 

this message usually indicates a bad structure, or more likely a bad initial
structure with too short minimization (VMD's NAMD Plot is nice to plot the
TOTAL energy from the minimization log to see if the minimization has
converged, don't forget to zoom in cause of the bad y-axis scale due high
initial peak). The first thing to try therefore is usually to increase the
number of minimization steps. But, as RATTLE only affects hydrogen atoms,
what you said : "atom 5 (CA)" may be wrong. Please remember that NAMD as
well as VMD start atom counting from zero, so you need to decrease all atom
numbers from the PDB when using them for any definition in the NAMD config,
like pulling constraints and also increase the numbers reported by NAMD to
map to the PDBs indices, so check that 1st maybe.

 

Good luck

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von MEHRAN MB
Gesendet: Freitag, 31. Mai 2013 18:33
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: fixed atom/Constraint failure in RATTLE algorithm/

 

Hi everyone,

 

I am trying to pull one end of my protein while the other end is fixed; But
as soon as it starts dynamic (right after energy minimization) and i get
this error:

ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.

it always happen for atom 5 or 7, please note that I am fixing atom 5 (CA)
which is bonded to atom 7 (CB). Somehow, I think I know where is the problem
since GPRESSURE in energy output is really high while PRESSURE is not. I
know GPRESSURE has something to do with Hydrogen, and both atom 5 and 7 have
Hydrogen bond and I am using rigid bond for H. Here is energy output

PRESSURE: 500 -6837.73 -1.68605 65.7687 -3.01476 -6863.58 60.0149 13.4313
87.7551 -7571.61
GPRESSURE: 500 -6767.67 9.31771 81.6069 -32.143 -6790.96 57.5848 15.5408
106.813 -7513.94
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 500 20791.7593 16518.8416 80.3129 37.9625
-763971.6307 48307.5924 0.0000 0.0000 0.0000
-678235.1620 0.0000 -678235.1620 -678235.1620 0.0000
-7090.9746 -7024.1899 2414412.0000 -7090.9746 -7024.1899

based on NAMD-mailing list suggestion i tried following solution but no
luck:
 

increasing margin or/and energy minimization time, checking for overlapped
atom s

I really appreciate your help,

Mehran

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