Re: Incompatibility between colvars and tclforces?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 30 2011 - 09:06:13 CDT

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
>>
>>
>

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