From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Mar 31 2011 - 02:27:40 CDT
Francesco,
I am happy that the initial problem was resolved ...
About the high energies, what happenns if you just run the colvars part
without RAMD ? Do you get these high energies ?
Vlad
On 03/30/2011 07:32 PM, Francesco Pietra wrote:
> > From the log for the last step (100), values of energy are normal when
> ramd is run without colvars:
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 100 10439.0858 17837.1373 9334.7397
> 750.4963 -763330.3414 55317.5845 0.0000
> 0.0000 144746.9679 -524904.3299 310.0220
> -669651.2978 -524636.7579 309.8461 -117.3802
> -29.1180 2165389.3570 -33.4127 -28.6342
>
> in contrast with the huge values when ramd-colvars is run (here I have
> added ramd output too, which may reveal anomalies):
> :
> LDB: =============== DONE WITH MIGRATION ================ 200.254
> TCL: RAMD FORCE: 100> LIGAND COM is: -2.73425127932 -0.339806653437
> -21.1803536289
> TCL: RAMD FORCE: 100> PROTEIN COM IS -1.65531722124 2.11186380535
> -22.5057988665
> TCL: RAMD FORCE: 100> EXTERNAL FORCE VECTOR (F): -30.2137023503
> 51.6457693126 -34.1484973099; ||F|| = 68.8932011604
> TCL: RAMD FORCE: 100> EXTERNAL FORCE DIRECTION (r): -0.438558549195
> 0.749649725121 -0.495672965325; ||r|| = 1.0
> TCL: RAMD FORCE: 100> TOTAL FORCE ON THE LIGAND COM IS:
> -4.94806180097 34.676069538 -38.361679672 (809.609866575)
> TCL: RAMD: 100 ***** EVALUATE 50 RAMD STEPS AT TIMESTEP 100 *****
> TCL: RAMD: 100>>> DISTANCE LIGAND COM - PPROTEIN COM IS:
> 2.98857688842; IT CHANGED BY -0.11815572734
> TCL: RAMD: 100>>> THE DISTANCE TRAVELLED BY THE LIGAND IS:
> 0.200611166485 (> 0.02)
> TCL: RAMD: 100>>> CONTINUE WITH 50 STEPS OF RAMD SIMULATION
> TCL: RAMD: 100>>> KEEP PREVIOUS ACCELERATION DIRECTION:
> -0.438558549195 0.749649725121 -0.495672965325; ||r|| = 1.0
> colvars: Saving collective variables state to "./ramd_acc-03.colvars.state".
> Info: Initial time: 4 CPUs 1.63275 s/step 18.8976 days/ns 328.624 MB memory
> TIMING: 100 CPU: 164.874, 1.6153/step Wall: 167.521, 1.63664/step, 0
> hours remaining, 328.624222 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG
> ENERGY: 100 10400.9726 17968.9046 9342.1516
> 767.3763 -762751.3280 54592.3878 0.0000
> 9999999999.9999 144779.9725 9999999999.9999 310.0927
> 9999999999.9999 9999999999.9999 309.8658 -254.1116
> -149.8729 2166090.0863 -121.2015 -118.3923
>
>
> The ligand binding site, from which ramd starts to push (with the bare
> 100 steps of this simulation the ligand did not move), is not very
> close to the regions affected by colvars. You may imagine a distance
> equivalent to the length of the ligand itself (a benzene ring with a
> few appendages). Could you imagine that colvars represent a barrier to
> the displacement of the ligand, leading to such high energies? We have
> no experience as yet with ramd plus colvars.
>
>
> Previous namd version was the same on all machines.
>
> thanks for your kind attention
>
> francesco
>
> ---------- Forwarded message ----------
> From: Francesco Pietra<chiendarret_at_gmail.com>
> Date: Wed, Mar 30, 2011 at 6:29 PM
> Subject: Re: namd-l: Incompatibility between colvars and tclforces?
> To: Jérôme Hénin<jhenin_at_ifr88.cnrs-mrs.fr>
> Cc: NAMD<namd-l_at_ks.uiuc.edu>, "Cojocaru,Vlad"
> <vlad.cojocaru_at_mpi-muenster.mpg.de>
>
>
> 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, Jérôme Hénin<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, 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
>>>>>
>>>>>
-- Dr. Vlad Cojocaru Max Planck Institute for Molecular Biomedicine Department of Cellular and Developmental Biology Roentgenstrasse 20 48149 Muenster, Germany tel: +49-251-70365-324 fax: +49-251-70365-399 email: vlad.cojocaru[at]mpi-muenster.mpg.de
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:03 CST