Re: Incompatibility between colvars and tclforces?

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Mar 30 2011 - 10:23:45 CDT

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, Jérôme Hénin <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 - 05:23:45 CST