Help

From: RICARDO VAZQUEZ (ricardo1v_at_yahoo.com)
Date: Thu May 03 2007 - 18:26:06 CDT

Next message: Monika Sharma: "Re: abrupt deviation in rmsd values"
Previous message: Stern, Julie: "error messages in log file"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

  I'm working with a protein from x-ray structure. I want to make a molecular dynamics calculation but the job only finish the molecular mechanics. Abort the calculations and sent the message :
  ERROR: Constraint failure in RATTLE algorithm for atom...!

  Please help me, at this moment I did everything, but nothing works, NAMD sent me the same error.
  How can I fix this problem?

  Thank you very much,

  Dr. Ricardo Vázquez
  Lab. de Química Hormonal,
Instituto de Investigaciones
Biomédicas, UNAM
C.P. 04510 MEXICO, D.F.
Tel. (52)55 56223815
Fax. (52)55 55500048

  This is the end of the output file:

  ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 5000 16285.2951 10458.5326 3281.4853 62.4406 -356783.6106 41445.5478 0.0073 0.0000 0.0000 -285250.3019 0.0000 -285250.3019 -285250.3019 0.0000 -4999.7935 -4969.9764 790209.0000 -4999.7935 -4969.9764

WRITING COORDINATES TO DCD FILE AT STEP 5000
WRITING COORDINATES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 5000
FINISHED WRITING RESTART VELOCITIES
TCL: Setting parameter fixedAtoms to off
REINITIALIZING VELOCITIES AT STEP 5000 TO 0 KELVIN.
TCL: Running for 250 steps
ERROR: Constraint failure in RATTLE algorithm for atom 8450!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6944!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5115!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 445.999023 CPUTime: 445.999023 Memory: 33759 kB
End of program

PS:

Read file <1z-gk1c-md.err> for stderr output of this job.

---------------------------------
Ahhh...imagining that irresistible "new car" smell?
Check outnew cars at Yahoo! Autos.

Next message: Monika Sharma: "Re: abrupt deviation in rmsd values"
Previous message: Stern, Julie: "error messages in log file"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:38 CST