Re: Incompatibility between colvars and tclforces?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 30 2011 - 11:29:15 CDT

Jerome:
ramd-colvars run together with the today Linux 64 nb. I should have
paid attention to the namd version...

There are 9999999999.999999999 values for MISC TOTAL POTENTIAL and
TOTAL.3, curios because the ensemble was finely equilibrated. But this
is a different affair.

Thanks a lot
francesco

On Wed, Mar 30, 2011 at 5:23 PM, J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> Francesco:
>
> I see the problem now. The error condition you are seeing disappeared
> from the CVS code on March 8, and you are using a slightly earlier
> version. Can you try the same input with version 2.8b1, or the current
> nightly build?
>
> Best,
> Jerome
>
> On 30 March 2011 16:06, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> Hi Jerome:
>> I discovered during the thread that I was unable to use colvars and
>> ramd in the same run. Confusion ensued, although it should have not
>> happened. Sorry.
>>
>> I have now repeated on a small machine the simulation from scratch,
>> re-starting from the equilibrated ensemble of a protein containing a
>> small organic ligand. Colvars were applied in that equilibration to
>> restrain the distances from a natural chloride ligand and its ligand
>> atoms (OH of neutral GLU, as well as NH of ARG and LYS). There is in
>> fact a chloride ligand for each protein subunit and - in  the absence
>> of the natural pool of chlorides - that chloride would go lost during
>> MD. In other words, in nature it is not always the same chloride that
>> occupies the site. That equilibration worked fine (after that you
>> recently corrected my errors in the colvars).
>>
>> My aim was then to displace the organic ligands from its binding site
>> in the protein by using the unbiased forces provided by RAMD. I
>> started from the above simulation with the unabridged conf file listed
>> below, where statements for RAMD were added. A few steps only were
>> requested.
>>
>> After the conf file listing I have reported the unabridged log
>> listing. I interpret that indicating that I can't use RAMD if colvars
>> are present, although that "design error" seems to indicate that my
>> setting up the simulation is incorrect.
>>
>> If the lines related to colvars in the conf file are commented out,
>> ramd runs fine, with no error or warning message (listing not
>> reported; can provide that if useful).
>>
>> The location of the RAMD tcl script is indicated in the conf file,
>> available in any namd2.8 installation.
>>
>>
>>
>> # Job
>> # System mod21-popc-AP1 TIP3-water-solvated, NaCl isotonic
>> # ramd with CLA-ligands colvars, PME following press-02.conf
>>
>> # forcefield
>> paratypecharmm on
>> parameters ./par_all27_prot_lipid.prm
>> parameters ./AP1.r.prm
>>
>>
>> # molecules
>> structure      ./complex.r.psf
>> coordinates    ./complex.r.pdb
>> bincoordinates  ./press-02.restart.coor
>> binvelocities   ./press-02.restart.vel
>> extendedSystem  ./press-02.restart.xsc
>>
>> # constraints
>> colvars      on # provide a colvarsConfig (and colvarsINput if restart)
>> colvarsConfig    ./CLA-ligands_colvars_press01.in
>> colvarsInput     ./press-02.restart.colvars.state
>>
>>
>> # constant temp control
>> langevin on
>> langevinTemp        310
>> langevinDamping     5
>> langevinHydrogen    off
>>
>> # constant pressure control
>> useGroupPressure    yes
>> useFlexibleCell     yes
>> useConstantRatio     no
>> LangevinPiston       on
>> LangevinPistonTarget  1.01325
>> LangevinPistonPeriod  200.
>> LangevinPistonDecay   100.
>> LangevinPistonTemp    310
>> UseConstantArea     yes
>>
>> # integrator
>> timestep            1.0  ;# 1fs/step
>> nonbondedFreq       1 ;# nonbonded forces every step
>> fullElectFrequency  5 ;# PME only every five step
>> stepspercycle       20  ;# redo pairlist every 20 steps
>>
>> # Approximations_1
>> # rigidBonds          all  ;# needed for 2fs/step
>> rigidBonds water
>> rigidTolerance      0.000001
>> exclude             scaled1-4
>> cutoff              12.0
>> switching           on
>> switchdist          10.0
>> pairlistdist        13.5 ;# cutoff +3.5
>> margin              3
>> 1-4scaling          1.0
>> PME                 yes
>> # cellBasisVector1    122.1    0.   0.
>> # cellBasisVector2     0.   119.2   0.
>> # cellBasisVector3     0.    0.  153.99
>> # Don't set the periodic cell basis if you have also specified an .xsc
>> # restart file
>> cellOrigin   -0.043044526129961014 -1.3494617938995361 -7.98848533630371
>> PMEGridSpacing      1.0
>>
>>
>> # output
>> outputName          ./ramd_acc-03
>> outputEnergies      10  # multiple of fullElectFrequency or viceversa
>> restartfreq         10
>> DCDfreq             100
>> binaryrestart       yes
>> binaryoutput        no
>> wrapNearest         on
>> wrapAll             on
>>
>>
>> #############################################################
>> #*** Random Acceleration Molecular Dynamics
>> *************************************
>>
>> source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl
>> #*** sources the wrapper script ramd-4.1.tcl;
>> #*** please change the directory '../scripts/' to '' ( the correct path );
>> #*** directory '' should contain the scripts: ramd-4.1.tcl,
>> ramd-4.1_script.tcl, and vectors.tcl
>>
>> ramd debugLevel                       0
>> #*** activates verbose output if set to something else than 0
>>
>> ramd ramdSteps                       50
>> #*** specifies the number of steps in 1 ramd stint;
>> #*** defaults to 50
>>
>> ramd accel                            0.3
>> #*** specifies the acceleration to be applied;
>> #*** defaults to 0.25 kcal/mol*A*amu
>>
>> ramd rMinRamd                         0.02
>> #*** specifies the minimum distance to be travelled by the ligand in 1
>> ramd stint;
>> #*** defaults to 0.01 Angstr
>>
>> ramd forceOutFreq                    50
>> #*** every 'forceOutFreq' steps detailed output of forces will be written;
>> #*** defaults to 0 (no detailed output)
>>
>> ramd maxDist                         50
>> #*** specifies the distance between the COMs of the ligand and the
>> protein when the simulation is stopped
>> #*** defaults to 50 Angstr (myoglobin max with 43 A)
>>
>> ramd firstProtAtom                    1
>> #*** specifies the index of the first protein atom
>> #*** defaults to 1 (assumes first atom in the system corresponds to
>> first protein atom
>>
>> ramd lastProtAtom                  20137
>> #*** specifies the index of the last protein atom
>> #*** required; simulation exits if this parameter is not set
>>
>> ramd firstRamdAtom                 219371
>> #*** specifies the index of the first ligand atom
>> #*** required; simulation exits if this parameter is not set
>>
>> ramd lastRamdAtom                  219393
>> #*** specifies the index of the last ligand atom
>> #*** required; simulation exits if this parameter is not set
>>
>> ramd ramdSeed                     14257
>> #*** specifies the seed for the random number generator (for the
>> generation of acceleration directions)
>> #*** defaults to 14253
>> #*** please change if you wish to run different trajectories
>> ######################
>> # Run protocol (steps multiple of stepspercycle)
>> seed              15341
>> numsteps              100
>> ******************************************************************************************
>>
>> Charmrun> charmrun started...
>> Charmrun> node programs all started
>> Charmrun> node programs all connected
>> Charmrun> adding client 0: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 1: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 2: "127.0.0.1", IP:127.0.0.1
>> Charmrun> adding client 3: "127.0.0.1", IP:127.0.0.1
>> Charmrun> Charmrun = 127.0.0.1, port = 56633
>> Charmrun> start 0 node program on localhost.
>> Charmrun> start 1 node program on localhost.
>> Charmrun> start 2 node program on localhost.
>> Charmrun> start 3 node program on localhost.
>> Charmrun> Waiting for 0-th client to connect.
>> Charmrun> Waiting for 1-th client to connect.
>> Charmrun> Waiting for 2-th client to connect.
>> Charmrun> client 1 connected (IP=127.0.0.1 data_port=50663)
>> Charmrun> client 2 connected (IP=127.0.0.1 data_port=57871)
>> Charmrun> client 3 connected (IP=127.0.0.1 data_port=53627)
>> Charmrun> Waiting for 3-th client to connect.
>> Charmrun> client 0 connected (IP=127.0.0.1 data_port=45416)
>> Charmrun> All clients connected.
>> Charmrun> IP tables sent.
>> Charm++: scheduler running in netpoll mode.
>> Charm++> Running on 1 unique compute nodes (4-way SMP).
>> Charm++> Cpu topology info:
>> PE to node map: 0 0 0 0
>> Node to PE map:
>> Chip #0: 0 1 2 3
>> Charm++> cpu topology info is gathered in 0.023 seconds.
>> Info: NAMD CVS-2011-02-14 for Linux-x86_64
>> Info:
>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>> Info:
>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>> Info: in all publications reporting results obtained with NAMD.
>> Info:
>> Info: Based on Charm++/Converse 60202 for net-linux-x86_64-iccstatic
>> Info: Built Mon Feb 14 02:16:25 CST 2011 by jim on lisboa.ks.uiuc.edu
>> Info: 1 NAMD  CVS-2011-02-14  Linux-x86_64  4    tya64  francesco
>> Info: Running on 4 processors.
>> Info: CPU topology information available.
>> Info: Charm++/Converse parallel runtime startup completed at 0.027072 s
>> Info: 1.63774 MB of memory in use based on CmiMemoryUsage
>> Info: Configuration file is ramd_acc-03.conf
>> Info: Working in the current directory
>> /home/francesco/work_hasic1a_GLUP_ASPP_allHSP_S-S/9.ramd_04-1.1
>> TCL: Suspending until startup complete.
>> Info: EXTENDED SYSTEM FILE   ./press-02.restart.xsc
>> Info: SIMULATION PARAMETERS:
>> Info: TIMESTEP               1
>> Info: NUMBER OF STEPS        100
>> Info: STEPS PER CYCLE        20
>> Info: PERIODIC CELL BASIS 1  122.1 0 0
>> Info: PERIODIC CELL BASIS 2  0 119.2 0
>> Info: PERIODIC CELL BASIS 3  0 0 148.634
>> Info: PERIODIC CELL CENTER   -0.0430445 -1.34946 -7.98849
>> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
>> Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
>> Info: LOAD BALANCER  Centralized
>> Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
>> Info: LDB PERIOD             4000 steps
>> Info: FIRST LDB TIMESTEP     100
>> Info: LAST LDB TIMESTEP     -1
>> Info: LDB BACKGROUND SCALING 1
>> Info: HOM BACKGROUND SCALING 1
>> Info: PME BACKGROUND SCALING 1
>> Info: MAX SELF PARTITIONS    20
>> Info: MAX PAIR PARTITIONS    8
>> Info: SELF PARTITION ATOMS   154
>> Info: SELF2 PARTITION ATOMS   154
>> Info: PAIR PARTITION ATOMS   318
>> Info: PAIR2 PARTITION ATOMS  637
>> Info: MIN ATOMS PER PATCH    100
>> Info: VELOCITY FILE          ./press-02.restart.vel
>> Info: CENTER OF MASS MOVING INITIALLY? NO
>> Info: DIELECTRIC             1
>> Info: EXCLUDE                SCALED ONE-FOUR
>> Info: 1-4 ELECTROSTATICS SCALED BY 1
>> Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
>> Info: DCD FILENAME           ./ramd_acc-03.dcd
>> Info: DCD FREQUENCY          100
>> Info: DCD FIRST STEP         100
>> Info: DCD FILE WILL CONTAIN UNIT CELL DATA
>> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
>> Info: NO VELOCITY DCD OUTPUT
>> Info: OUTPUT FILENAME        ./ramd_acc-03
>> Info: RESTART FILENAME       ./ramd_acc-03.restart
>> Info: RESTART FREQUENCY      10
>> Info: BINARY RESTART FILES WILL BE USED
>> Info: SWITCHING ACTIVE
>> Info: SWITCHING ON           10
>> Info: SWITCHING OFF          12
>> Info: PAIRLIST DISTANCE      13.5
>> Info: PAIRLIST SHRINK RATE   0.01
>> Info: PAIRLIST GROW RATE     0.01
>> Info: PAIRLIST TRIGGER       0.3
>> Info: PAIRLISTS PER CYCLE    2
>> Info: PAIRLISTS ENABLED
>> Info: MARGIN                 3
>> Info: HYDROGEN GROUP CUTOFF  2.5
>> Info: PATCH DIMENSION        19
>> Info: ENERGY OUTPUT STEPS    10
>> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>> Info: TIMING OUTPUT STEPS    100
>> Info: TCL GLOBAL FORCES ACTIVE
>> Info: TCL GLOBAL FORCES SCRIPT
>> /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1_script.tcl
>> Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
>> Info: COLLECTIVE VARIABLES CONFIGURATION   ./CLA-ligands_colvars_press01.in
>> Info: COLLECTIVE VARIABLES RESTART INFORMATION
>> ./press-02.restart.colvars.state
>> Info: LANGEVIN DYNAMICS ACTIVE
>> Info: LANGEVIN TEMPERATURE   310
>> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
>> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
>> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
>> Info:        TARGET PRESSURE IS 1.01325 BAR
>> Info:     OSCILLATION PERIOD IS 200 FS
>> Info:             DECAY TIME IS 100 FS
>> Info:     PISTON TEMPERATURE IS 310 K
>> Info:       PRESSURE CONTROL IS GROUP-BASED
>> Info:    INITIAL STRAIN RATE IS 1.30719e-05 3.88275e-05 2.39687e-06
>> Info:       CELL FLUCTUATION IS ANISOTROPIC
>> Info:     CONSTANT AREA PRESSURE CONTROL ACTIVE
>> Info: PARTICLE MESH EWALD (PME) ACTIVE
>> Info: PME TOLERANCE               1e-06
>> Info: PME EWALD COEFFICIENT       0.257952
>> Info: PME INTERPOLATION ORDER     4
>> Info: PME GRID DIMENSIONS         128 120 160
>> Info: PME MAXIMUM GRID SPACING    1
>> Info: Attempting to read FFTW data from
>> FFTW_NAMD_CVS-2011-02-14_Linux-x86_64.txt
>> Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
>> Info: Writing FFTW data to FFTW_NAMD_CVS-2011-02-14_Linux-x86_64.txt
>> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      5
>> Info: USING VERLET I (r-RESPA) MTS SCHEME.
>> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
>> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
>> Info: RIGID BONDS TO HYDROGEN : WATER
>> Info:         ERROR TOLERANCE : 1e-06
>> Info:          MAX ITERATIONS : 100
>> Info: RIGID WATER USING SETTLE ALGORITHM
>> Info: RANDOM NUMBER SEED     15341
>> Info: USE HYDROGEN BONDS?    NO
>> Info: COORDINATE PDB         ./complex.r.pdb
>> Info: STRUCTURE FILE         ./complex.r.psf
>> Info: PARAMETER file: CHARMM format!
>> Info: PARAMETERS             ./par_all27_prot_lipid.prm
>> Info: PARAMETERS             ./AP1.r.prm
>> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
>> Info: BINARY COORDINATES     ./press-02.restart.coor
>> Info: SUMMARY OF PARAMETERS:
>> Info: 195 BONDS
>> Info: 485 ANGLES
>> Info: 608 DIHEDRAL
>> Info: 54 IMPROPER
>> Info: 6 CROSSTERM
>> Info: 130 VDW
>> Info: 0 VDW_PAIRS
>> Info: TIME FOR READING PSF FILE: 2.80614
>> Info: TIME FOR READING PDB FILE: 0.958783
>> Info:
>> Info: Reading from binary file ./press-02.restart.coor
>> Info: ****************************
>> Info: STRUCTURE SUMMARY:
>> Info: 219393 ATOMS
>> Info: 156441 BONDS
>> Info: 119832 ANGLES
>> Info: 82263 DIHEDRALS
>> Info: 3446 IMPROPERS
>> Info: 1264 CROSSTERMS
>> Info: 0 EXCLUSIONS
>> Info: 188277 RIGID BONDS
>> Info: 469902 DEGREES OF FREEDOM
>> Info: 77450 HYDROGEN GROUPS
>> Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
>> Info: 77450 MIGRATION GROUPS
>> Info: 4 ATOMS IN LARGEST MIGRATION GROUP
>> Info: TOTAL MASS = 1.34691e+06 amu
>> Info: TOTAL CHARGE = -0.000173653 e
>> Info: MASS DENSITY = 1.03392 g/cm^3
>> Info: ATOM DENSITY = 0.101417 atoms/A^3
>> Info: *****************************
>> Info:
>> Info: Entering startup at 4.02434 s, 57.3401 MB of memory in use
>> Info: Startup phase 0 took 0.0625331 s, 57.3364 MB of memory in use
>> Info: Startup phase 1 took 1.82799 s, 95.2431 MB of memory in use
>> Info: Startup phase 2 took 0.0359881 s, 96.9225 MB of memory in use
>> Info: Startup phase 3 took 0.0506589 s, 96.9223 MB of memory in use
>> Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 7 (PERIODIC)
>> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
>> Info: Reading from binary file ./press-02.restart.vel
>> Info: REMOVING COM VELOCITY 0.00292499 0.0305455 0.0250787
>> Info: LARGEST PATCH (51) HAS 943 ATOMS
>> Info: Startup phase 4 took 0.289306 s, 124.16 MB of memory in use
>> Info: PME using 4 and 4 processors for FFT and reciprocal sum.
>> Info: PME GRID LOCATIONS: 0 1 2 3
>> Info: PME TRANS LOCATIONS: 0 1 2 3
>> Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
>> Info: Startup phase 5 took 0.0680361 s, 129.046 MB of memory in use
>> Info: Startup phase 6 took 0.128015 s, 109.221 MB of memory in use
>> LDB: Central LB being created...
>> Info: Startup phase 7 took 1.27197 s, 109.369 MB of memory in use
>> Info: CREATING 16022 COMPUTE OBJECTS
>> Info: useSync: 1 useProxySync: 0
>> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
>> Info: NONBONDED TABLE SIZE: 769 POINTS
>> TCL: RAMD:
>> TCL: RAMD: -------------------------------------------------------------------
>> TCL: RAMD: Random Acceleration Molecular Dynamics Simulation version 4.1
>> TCL: RAMD: -------------------------------------------------------------------
>> TCL: RAMD:
>> TCL: RAMD:                   mdSteps = 0
>> TCL: RAMD:                     accel = 0.3
>> TCL: RAMD:                  ramdSeed = 14257
>> TCL: RAMD:              forceOutFreq = 50
>> TCL: RAMD:                   maxDist = 50
>> TCL: RAMD:             firstProtAtom = 1
>> TCL: RAMD:                  rMinRamd = 0.02
>> TCL: RAMD:                debugLevel = 0
>> TCL: RAMD:                   mdStart = no
>> TCL: RAMD:                 ramdSteps = 50
>> TCL: RAMD:             firstRamdAtom = 219371
>> TCL: RAMD:              lastRamdAtom = 219393
>> TCL: RAMD:              lastProtAtom = 20137
>> TCL: RAMD: Pure RAMD simulation is performed
>> TCL: RAMD:
>> TCL: RAMD: Atoms subject to the random acceleration are: 219371 219372
>> 219373 219374 219375 219376 219377 219378 219379 219380 219381 219382
>> 219383 219384 219385 219386 219387 219388 219389 219390 219391 219392
>> 219393
>> colvars: ----------------------------------------------------------------------
>> colvars: Initializing the collective variables module, version 2011-01-03.
>> colvars: # analysis = off [default]
>> colvars: # colvarsTrajFrequency = 100
>> colvars: # colvarsRestartFrequency = 200
>> colvars: # colvarsTrajAppend = off [default]
>> colvars: The restart output state file will be
>> "./ramd_acc-03.restart.colvars.state".
>> colvars: The final output state file will be "./ramd_acc-03.colvars.state".
>> colvars: The trajectory file will be "./ramd_acc-03.colvars.traj".
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar1
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 2 initialized: total mass = 28.014.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar2
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 14.007.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   Warning: found more than one instance of "outputSystemForce".
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar3
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 15.999.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar4
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 2 initialized: total mass = 28.014.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar5
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 14.007.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   Warning: found more than one instance of "outputSystemForce".
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar6
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 15.999.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar7
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 2 initialized: total mass = 28.014.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar8
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 14.007.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new collective variable.
>> colvars:   # name = colvar9
>> colvars:   Initializing a new "distance" component.
>> colvars:     # componentCoeff = 1 [default]
>> colvars:     # componentExp = 1 [default]
>> colvars:     # period = 0 [default]
>> colvars:     # wrapAround = 0 [default]
>> colvars:     # forceNoPBC = off [default]
>> colvars:     # oneSiteSystemForce = off [default]
>> colvars:       Initializing atom group "group1".
>> colvars:       Atom group "group1" defined, 1 initialized: total mass = 35.45.
>> colvars:       Initializing atom group "group2".
>> colvars:       Atom group "group2" defined, 1 initialized: total mass = 15.999.
>> colvars:   All components initialized.
>> colvars:   # width = 1
>> colvars:   # lowerBoundary = -10
>> colvars:   # lowerWallConstant = 100
>> colvars:   # lowerWall = -5
>> colvars:   # upperBoundary = 10
>> colvars:   # upperWallConstant = 100
>> colvars:   # upperWall = 5
>> colvars:   # expandBoundaries = off [default]
>> colvars:   # extendedLagrangian = off [default]
>> colvars:   # outputValue = on [default]
>> colvars:   # outputVelocity = off [default]
>> colvars:   # outputSystemForce = on
>> colvars:   # outputAppliedForce = off [default]
>> colvars: ----------------------------------------------------------------------
>> colvars: Collective variables initialized, 9 in total.
>> colvars: ----------------------------------------------------------------------
>> colvars:   Initializing a new "harmonic" instance.
>> colvars:   # name = CLA_harmonic
>> colvars:   # colvars = { colvar1, colvar2, colvar3, colvar4, colvar5,
>> colvar6, colvar7, colvar8, colvar9 }
>> colvars:   # forceConstant = 5
>> colvars:   # centers = { 3.6, 4.9, 3, 3.2, 3, 4, 3.5, 3.1, 5 }
>> colvars:   # targetCenters = { 3.6, 4.9, 3, 3.2, 3, 4, 3.5, 3.1, 5 } [default]
>> colvars:   # targetForceConstant = 0 [default]
>> colvars: ----------------------------------------------------------------------
>> colvars: Collective variables biases initialized, 1 in total.
>> colvars: ----------------------------------------------------------------------
>> colvars: Restarting from file "./press-02.restart.colvars.state".
>> colvars:   Restarting collective variable "colvar1" from value: 3.48985
>> colvars:   Restarting collective variable "colvar2" from value: 4.50437
>> colvars:   Restarting collective variable "colvar3" from value: 3.32463
>> colvars:   Restarting collective variable "colvar4" from value: 3.04155
>> colvars:   Restarting collective variable "colvar5" from value: 2.99285
>> colvars:   Restarting collective variable "colvar6" from value: 3.1526
>> colvars:   Restarting collective variable "colvar7" from value: 3.20845
>> colvars:   Restarting collective variable "colvar8" from value: 3.11906
>> colvars:   Restarting collective variable "colvar9" from value: 5.10255
>> colvars:   Restarting harmonic bias "CLA_harmonic".
>> colvars: ----------------------------------------------------------------------
>> colvars: Collective variables module initialized.
>> colvars: ----------------------------------------------------------------------
>> Info: Startup phase 8 took 0.242676 s, 125.065 MB of memory in use
>> Info: Startup phase 9 took 0.000263929 s, 133.014 MB of memory in use
>> Info: Finished startup at 8.00178 s, 133.014 MB of memory in use
>>
>> FATAL ERROR: Due to a design error, GlobalMasterServer does not
>> support individual atom requests from multiple global force clients on
>> parallel runs.
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Due to a design error, GlobalMasterServer does
>> not support individual atom requests from multiple global force
>> clients on parallel runs.
>>
>> [0] Stack Traceback:
>>  [0:0] CmiAbort+0x7b  [0xb683cd]
>>  [0:1] _Z8NAMD_diePKc+0x62  [0x525722]
>>  [0:2] _ZN18GlobalMasterServer11callClientsEv+0x408  [0x82efd8]
>>  [0:3] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x6f7
>>  [0x82e67f]
>>  [0:4] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x12
>>  [0x5a6afe]
>>  [0:5] _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0xf
>>  [0x5a6ae9]
>>  [0:6] CkDeliverMessageFree+0x21  [0xaafe43]
>>  [0:7] _Z15_processHandlerPvP11CkCoreState+0x711  [0xaaeceb]
>>  [0:8] CsdScheduleForever+0xa5  [0xb6ef6b]
>>  [0:9] CsdScheduler+0x1c  [0xb6eb6c]
>>  [0:10] _ZN7BackEnd7suspendEv+0xb  [0x52de7d]
>>  [0:11] _ZN9ScriptTcl3runEv+0x108  [0xa03c4a]
>>  [0:12] _Z18after_backend_initiPPc+0x3f2  [0x529a52]
>>  [0:13] main+0x3a  [0x52962a]
>>  [0:14] __libc_start_main+0xe6  [0x7f294f9361a6]
>>  [0:15] _ZNSt8ios_base4InitD1Ev+0x52  [0x52501a]
>> Fatal error on PE 0> FATAL ERROR: Due to a design error,
>> GlobalMasterServer does not support individual atom requests from
>> multiple global force clients on parallel runs.
>>
>>
>> Thanks
>> francesco
>>
>>
>> On Wed, Mar 30, 2011 at 1:23 PM, J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>>> Hi Francesco,
>>>
>>> In my latest tests, colvars and TclForces worked fine together. I am
>>> confused about the recent thread you started, where several different
>>> things seemed to be happening at once.
>>> Can you please describe precisely a test case that failed?
>>>
>>> Best,
>>> Jerome
>>>
>>> On 30 March 2011 12:04, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>>> Hi:
>>>>  I have found obstacles in trying to use colvars while applying
>>>> tcforces (of course to different atoms than those involved in
>>>> colvars). I have posted the problem in the last few days, yesterday
>>>> more definitely.
>>>>
>>>> Although it may be too early to hope for advice about my question, I
>>>> am wondering now whether there may be a general incompatibility
>>>> between colvars and tclforces.  My aim is to restraint some distances
>>>> in the protein and its ligands while applying tcl forces to another
>>>> ligand inside the protein. If the combination colvars-tclforces can
>>>> not be practicized, is that a different approach to the problem? This
>>>> implies that restraining those distances is a sine-qua-non condition
>>>> for running a correct MD.
>>>>
>>>> thanks
>>>> francesco pietra
>>>>
>>>>
>>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:52 CST