From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Mar 26 2010 - 06:34:11 CDT
Hi Ferenc,
What the error message is trying to say, although not explicitly
enough apparently, is that the colvars won't work during energy
minimization.
Jerome
On 26 March 2010 10:45, Ferenc Ötvös, PhD <otvos_at_brc.hu> wrote:
> Dear Members,
>
> Possibly I am not using the colvar module the right way, but I am not able
> to use the colvar functionality in NAMD 2.7b2.
> The system has 4 segments, of witch 4 atoms (1 from each segment) would be
> restrained by a dihedral angle. It did not work either in autoimd session or
> in a background run.
>
> I should be very grateful if someone could help me with this issue.
> Thanks
> Ferenc Otvos
>
>
>
> Some details that may be essential follows below:
>
> NAMD config file:
>
> set paramfile_list {par_all27_prot_lipid_na.inp}
> set imdport 6150
> set sim_mode equilibrate
> set namdoutputrate 1
> set dcdfreq 0
> set temperature 300
> set minimizesteps 100
> set runsteps 1000000
> set MYSCRIPT {}
> ##############################################################3
> ##
> ## This file is used as a template for running NAMD jobs
> ## When this file is run, the following Tcl variables will
> ## have been initialized to appropriate values:
> ## imdport, minimizesteps, runsteps, paramfile_list
> ##
> ###############################################################3
>
> # Input
> structure autoimd.psf
> coordinates autoimd.pdb
> paraTypeCharmm on
> foreach paramfile $paramfile_list {
> parameters $paramfile
> }
> temperature $temperature
>
> # Output
> if { $dcdfreq > 0 } {
> DCDFile autoimd.dcd
> DCDFreq $dcdfreq
> }
>
> # IMD parameters
> imdon on
> imdport $imdport
> imdfreq $namdoutputrate
> imdwait on
>
>
> # Fixed Atoms
> fixedAtoms on
> fixedAtomsFile autoimd.pdb
> fixedAtomsCol B
>
>
> # Collective variables section
> colvars on
> colvarsConfig colvars.config
>
>
> # Integrator and dynamics parameters
> rigidbonds all
> timestep 2.0
> nonBondedFreq 1
> stepsPerCycle 10
>
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> langevin on
> langevinDamping 3
> langevinTemp $temperature
> langevinHydrogen no
>
>
> # Output options
> outputname autoimd_out
> outputTiming 1000
>
> eval $MYSCRIPT
>
> # This line permits AutoIMD to connect to jobs running on remote machines
> print "AUTOIMD HOST: [info hostname] PID: [pid]"
>
> # Run simulation
> minimize $minimizesteps
> reinitvels $temperature
> run $runsteps
>
>
> colvar config file:
>
> # collective variables config file: dihedrals
> colvarsTrajFrequency 100 # output values every 100 steps
> colvarsRestartFrequency 10000
> analysis on
>
> colvar {
> name dihedral1 # needed to identify the variable
> outputSystemForce no # report also the system force on this colvar
> # (in addition to the current value)
>
> dihedral {
> group1 {
> atomNumbers 5
> }
> group2 {
> atomNumbers 1921
> }
> group3 {
> atomNumbers 3837
> }
> group4 {
> atomNumbers 5753
> }
> }
> }
>
> harmonic {
> name torsions
> colvars {
> dihedral1
> }
> centers {
> 0.0
> }
> forceConstant 5
> }
>
>
> Part of the log file:
>
> Info: STRUCTURE SUMMARY:
> Info: 7665 ATOMS
> Info: 7740 BONDS
> Info: 14000 ANGLES
> Info: 20436 DIHEDRALS
> Info: 1176 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 0 FIXED ATOMS
> Info: 3864 RIGID BONDS
> Info: 0 RIGID BONDS BETWEEN FIXED ATOMS
> Info: 19131 DEGREES OF FREEDOM
> Info: 3801 HYDROGEN GROUPS
> Info: 0 HYDROGEN GROUPS WITH ALL ATOMS FIXED
> Info: TOTAL MASS = 54223.9 amu
> Info: TOTAL CHARGE = -6 e
> Info: *****************************
> Info:
> Info: Entering startup at 348502 s, 3.82005 MB of memory in use
> Info: Startup phase 0 took 0.00030351 s, 3.82006 MB of memory in use
> Info: Startup phase 1 took 0.0280507 s, 5.72552 MB of memory in use
> Info: Startup phase 2 took 0.000191086 s, 5.78677 MB of memory in use
> Info: PATCH GRID IS 3 BY 3 BY 4
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0.0507798 -0.037221 -0.0543319
> Info: LARGEST PATCH (12) HAS 573 ATOMS
> Info: CREATING 487 COMPUTE OBJECTS
> Info: Startup phase 3 took 0.0231574 s, 6.77894 MB of memory in use
> Info: Startup phase 4 took 0.000164252 s, 6.77883 MB of memory in use
> Info: Startup phase 5 took 0.000162553 s, 6.77872 MB of memory in use
> LDB: Measuring processor speeds ... Done.
> Info: Startup phase 6 took 0.000234515 s, 6.77962 MB of memory in use
> Info: CREATING 487 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.44089e-16 AT 0.121031
> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04097e-13 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974
> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
> Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
> Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
> Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
> Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
> Info: Interactive MD listening on port 6150.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 20090807.
> colvars: # analysis = on
> colvars: # colvarsTrajFrequency = 100
> colvars: # colvarsRestartFrequency = 10000
> colvars: The trajectory file will be "autoimd_out.colvars.traj".
> colvars: The final output state file will be "autoimd_out.colvars.state".
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = dihedral1
> colvars: Initializing a new "dihedral" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # oneSiteSystemForce = off [default]
> 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 = 1 [default]
> colvars: # lowerBoundary = 0 [default]
> colvars: # lowerWallConstant = 0 [default]
> colvars: # upperBoundary = 0 [default]
> colvars: # upperWallConstant = 0 [default]
> colvars: # expandBoundaries = off [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = off
> colvars: # outputAppliedForce = off [default]
> colvars: # runAve = off [default]
> colvars: # corrFunc = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = torsions
> colvars: # colvars = { dihedral1 }
> colvars: # forceConstant = 5
> colvars: # centers = { 0 }
> colvars: # targets = { 0 } [default]
> colvars: # forceConstantTarget = 0 [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables biases initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module initialized.
> colvars:
> ----------------------------------------------------------------------
> Info: Startup phase 7 took 0.0179073 s, 9.07521 MB of memory in use
> Info: Startup phase 8 took 0.000470199 s, 13.7061 MB of memory in use
> Info: Finished startup at 348502 s, 13.7061 MB of memory in use
>
> TCL: Minimizing for 100 steps
> Info: INTERACTIVE MD AWAITING CONNECTION
> Info: IMD connection opened
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
>
> ENERGY: 0 326.9165 8396.1314 2375.9181 12.6324
> -1438.2852 1390925468.8494 0.0000 0.0000
> 0.0000 1390935142.1626 0.0000 1390935142.1626 1390935142.1626
> 0.0000
>
> MINIMIZER SLOWLY MOVING 14 ATOMS WITH BAD CONTACTS DOWNHILL
> colvars: Error: cannot find the total force of atom 5. Is energy
> minimization (instead of MD) enabled?
> colvars: If this error message is unclear, try recompile with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
>
>
> Charm++ fatal error:
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
> [0] Stack Traceback:
> [0] _ZN12colvarmodule11fatal_errorERKSs+0xf [0x83bcca1]
> [1] _ZThn8_N16colvarproxy_namd9calculateEv+0xd [0x844a5c1]
> [2] _ZN18GlobalMasterServer11callClientsEv+0x42f [0x83a6563]
> [3] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x5ec
> [0x83a5c0c]
>
> --------------------------------------------------
>
> I tried couple of different variations in configs, but the key error was all
> the time:
> colvars: Error: cannot find the total force of atom 5......
>
>
>
>
> Ferenc Otvos, PhD
> Institute of Biochemistry
> Biological Research Center, Szeged, Hungary
> Temesvari krt. 62, Szeged, Hungary, H-6726
>
> ----------------------------------------------------------------
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>
>
>
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