RE: error in writing colvars state file

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Jun 04 2015 - 16:30:07 CDT

I forgot to list that I am using namd29 on a linux cluster.
Brian

________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Bennion, Brian [bennion1_at_llnl.gov]
Sent: Thursday, June 04, 2015 2:24 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: error in writing colvars state file

Hello,

I am trying a test of the colvars dihedral component. My files are based on those from NANMA tutorial.
The calculation stops when it tries to write for the first time. The job seems to have forgotten the name of the some of the output files. I do get output in the *.pmf file, however.

colvars: Writing the state file "".
colvars: Error: in writing restart file.

The colvars section of the log file is listed below and my colvars config file is listed after that.

I have searched the mail lists for namd and the tutorials without a hit on this type of error. I may have missed something. It just seems this error is an omission on my part somewhere.
Brian

colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # colvarsTrajAppend = off [default]
colvars: The final output state file will be "apo2apoFlipped.colvars.state".
colvars: The trajectory file will be "apo2apoFlipped.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = chi1
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # oneSiteSystemForce = on
colvars: Computing system force on group 1 only
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 14.007.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group3".
colvars: Atom group "group3" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group4".
colvars: Atom group "group4" defined, 1 initialized: total mass = 12.011.
colvars: All components initialized.
colvars: # width = 5
colvars: # lowerBoundary = -70
colvars: # lowerWallConstant = 0.2
colvars: # lowerWall = -70 [default]
colvars: # upperBoundary = 50
colvars: # upperWallConstant = 0.2
colvars: # upperWall = 50 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = chi2
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # oneSiteSystemForce = on
colvars: Computing system force on group 1 only
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group3".
colvars: Atom group "group3" defined, 1 initialized: total mass = 12.011.
colvars: Initializing atom group "group4".
colvars: Atom group "group4" defined, 1 initialized: total mass = 12.011.
colvars: All components initialized.
colvars: # width = 5
colvars: # lowerBoundary = -85
colvars: # lowerWallConstant = 0.2
colvars: # lowerWall = -85 [default]
colvars: # upperBoundary = 120
colvars: # upperWallConstant = 0.2
colvars: # upperWall = 120 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = "metadynamics1" [default]
colvars: # colvars = { chi1, chi2 }
colvars: # hillWeight = 0.01 [default]
colvars: # newHillFrequency = 1000 [default]
colvars: # hillWidth = 2
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 1000 [default]
colvars: # rebinGrids = off [default]
colvars: # keepHills = off [default]
colvars: # dumpFreeEnergyFile = on [default]
colvars: # saveFreeEnergyFile = off [default]
colvars: # multipleReplicas = off [default]
colvars: # writeHillsTrajectory = off [default]
colvars: # wellTempered = off [default]
colvars: # biasTemperature = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------

Info: Benchmark time: 4 CPUs 0.166071 s/step 1.92212 days/ns 209.996 MB memory
ENERGY: 400 19345.1317 14540.9237 4844.9631 283.0363 -239046.3038 20842.1334 0.0000 0.0040 48720.4981 -130469.6134 295.8986 -179190.1115 -130029.8202 295.7436 84.3780 114.7165 519417.6247 13.0873 13.9719

colvars: Writing the state file "".
colvars: Error: in writing restart file.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.

[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x72 [0x54be02]
  [0:1] _ZN16colvarproxy_namd11fatal_errorERKSs+0x70 [0x9802d0]
  [0:2] _ZN12colvarmodule4calcEv+0x4e8 [0x8d9f48]
  [0:3] _ZThn16_N16colvarproxy_namd9calculateEv+0x4a8 [0x97d958]
  [0:4] _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x8c [0x8b039c]
  [0:5] _ZN18GlobalMasterServer11callClientsEv+0x863 [0x8b3513]
  [0:6] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x64c [0x8b27ec]
  [0:7] _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0x18 [0x5c2338]
  [0:8] CkDeliverMessageFree+0x96 [0xb44bd6]
  [0:9] _Z15_processHandlerPvP11CkCoreState+0x7d3 [0xb44213]
  [0:10] CsdScheduler+0x41a [0xcb483a]
  [0:11] _ZN7BackEnd7suspendEv+0xb [0x55639b]
  [0:12] _ZN9ScriptTcl3runEv+0x372 [0xa87522]
  [0:13] main+0x4f7 [0x5502a7]
  [0:14] __libc_start_main+0xfd [0x2aaaac244d5d]
  [0:15] [0x50dd09]
colvarsTrajFrequency 500
colvarsRestartFrequency 500

colvar {
  name chi1

  width 5.0
  lowerboundary -70
  upperboundary 50
  lowerWallConstant 0.2
  upperWallConstant 0.2

  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 3487
    }
    group2 {
      atomnumbers 3489
    }
    group3 {
      atomnumbers 3491
    }
    group4 {
      atomnumbers 3494
    }
  }
}

colvar {
  name chi2

  width 5.0
  lowerboundary -85
  upperboundary 120
  lowerWallConstant 0.2
  upperWallConstant 0.2

  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 3489
    }
    group2 {
      atomnumbers 3491
    }
    group3 {
      atomnumbers 3494
    }
    group4 {
      atomnumbers 3495
    }
  }
}

metadynamics {
  colvars chi1 chi2
  hillWidth 2
}

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