CCL: problem in running configuration file using NAMD

[Vincent Leroux <vincent.leroux%a%loria.fr>]

 Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr]
 Hi,
 Look at the bottom of the parameter file. What you have been doing is:
 - 100 minimization steps
 - assign velocities for 302 K all of a sudden
 - 2500 steps of MD
100 steps of minimization is probably not enough, but this is not the
 problem. You just go straight from minimization to MD: MD is started
 with a random set of velocities averaged to T = 302 K, resulting in
 your
 system being literally torn apart. The RATTLE algorithm tries to
 compensate for abnormal bond lengths occurring at the very first MD
 step, but of course it fails.
You should do some equilibration after minimization... The comment at
 the beginning of your parameter file is mistaking: it says
 "minimization
 and equilibration" and below I see the (right) comment "do
 langevin
 dynamics". Seems like this input file was messed up by careless
 copy-paste operations.
 Regards
 VL
 Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com a écrit :
>  Sent to CCL by: "neha  khan" [diya.khan.05~~gmail.com]
>  Respected Sir,
>  When i run minimization, the program stopped abnormally. What is wrong with my
>  file?
>  REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN.
>  TCL: Running for 2500 steps
>  ERROR: Constraint failure in RATTLE algorithm for atom 2775!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 2729!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1739!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 2926!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 6029!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 2398!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 2202!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 3201!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 5028!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 2390!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 553!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 3136!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 4966!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1588!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 4118!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1275!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 771!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1069!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 4008!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 867!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 919!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 3447!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 6355!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 4747!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 332!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 6837!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 82!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1542!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1254!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 9773!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 1193!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 3739!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 9465!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 953!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 10527!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 3678!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 117!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8745!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 9881!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 10838!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 7839!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8262!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 9955!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 10206!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8881!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 10080!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8404!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8589!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8450!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8308!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8580!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Constraint failure in RATTLE algorithm for atom 8572!
>  ERROR: Constraint failure; simulation has become unstable.
>  ERROR: Exiting prematurely; see error messages above.
>  ====================================================
>  WallClock: 74.289345  CPUTime: 74.199997  Memory: 99.713013 MB
>  Program finished.
>  execve failed to start process "namd2" with status: -1
>  execve failed to start process "namd2" with status: -1
>  execve failed to start process "namd2" with status: -1
>  execve failed to start process "namd2" with status: -1
>  Killed
>  Below is my configuration file:
>  #############################################################
>  ## JOB DESCRIPTION                                         ##
>  #############################################################
>  # Minimization and Equilibration of
>  # pgl in a Water Sphere
>  #############################################################
>  ## ADJUSTABLE PARAMETERS                                   ##
>  #############################################################
>  structure          ../common/pgl_ws.psf
>  coordinates        ../common/pgl_ws.pdb
>  set temperature    302
>  set outputname     pgl_ws_eq
>  firsttimestep      0
>  #############################################################
>  ## SIMULATION PARAMETERS                                   ##
>  #############################################################
>  # Input
>  paraTypeCharmm	    on
>  parameters          ../common/par_all27_prot_lipid.inp
>  temperature         $temperature
>  # Force-Field Parameters
>  exclude             scaled1-4
>  1-4scaling          1.0
>  cutoff              12.
>  switching           on
>  switchdist          10.
>  pairlistdist        13.5
>  # Integrator Parameters
>  timestep            2.0  ;# 2fs/step
>  rigidBonds          all  ;# needed for 2fs steps
>  nonbondedFreq       1
>  fullElectFrequency  2
>  stepspercycle       10
>  # Constant Temperature Control
>  langevin            on    ;# do langevin dynamics
>  langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
>  langevinTemp        $temperature
>  langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>  # Output
>  outputName          $outputname
>  restartfreq         500     ;# 500steps = every 1ps
>  dcdfreq             250
>  outputEnergies      100
>  outputPressure      100
>  #############################################################
>  ## EXTRA PARAMETERS                                        ##
>  #############################################################
>  # Spherical boundary conditions
>  sphericalBC         on
>  sphericalBCcenter   30.3081743413, 28.8049907121, 15.353994423
>  sphericalBCr1       26.0
>  sphericalBCk1       10
>  sphericalBCexp1     2
>  #############################################################
>  ## EXECUTION SCRIPT                                        ##
>  #############################################################
>  # Minimization
>  minimize            100
>  reinitvels          $temperature
>  run 2500 ;# 5ps>