From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Jun 05 2015 - 05:33:07 CDT
Hi Brian,
Can you test the same input with namd 2.10?
Thanks,
Jerome
On 4 June 2015 at 23:30, Bennion, Brian <bennion1_at_llnl.gov> wrote:
> 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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