Re: RAMD Setting parameter TclForces from script failed

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Apr 13 2011 - 08:33:57 CDT

The multiple global force clients issue was fixed in 2.8b1, with a bug in
the new implementation fixed March 27.

-Jim

On Tue, 29 Mar 2011, Francesco Pietra wrote:

> Hello Jim:
> It starts to become clear this morning (hopefully). It seems to me
> that the problem is the simultaneous presence of colvars and ramd (a
> situation that I have emphasized on previous posts, without having any
> reason for that). Both involve individual atom requests, which is not
> allowed in parallel simulations.
>
> Thus, sourcing ramd script from only the ramd portion of namd conf
> file, and having "numsteps" (probably the same having "run") at the
> end of namd conf file (after ramd), the error is:
>
> FATAL ERROR: Due to a design error, GlobalMasterServer does not
> support individual atom requests from multiple global force clients on
> parallel runs.
>
> Here the relevant portions of the log file, where I have shortened the
> portion related to colvars:
>
> arm++> cpu topology info is gathered in 0.001 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 0.078851 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 15343
> 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: 2.7509
> Info: TIME FOR READING PDB FILE: 0.902384
> 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 3.82823 s, 57.3364 MB of memory in use
> Info: Startup phase 0 took 0.192449 s, 57.336 MB of memory in use
> Info: Startup phase 1 took 1.98068 s, 95.3553 MB of memory in use
> Info: Startup phase 2 took 0.056417 s, 97.0344 MB of memory in use
> Info: Startup phase 3 took 0.0479629 s, 97.0343 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 0.242286 s, 124.273 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 0.0777831 s, 129.158 MB of memory in use
> Info: Startup phase 6 took 0.124777 s, 109.334 MB of memory in use
> LDB: Central LB being created...
> Info: Startup phase 7 took 1.33913 s, 109.481 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: # 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 0.171692 s, 125.178 MB of memory in use
> Info: Startup phase 9 took 0.000221014 s, 133.126 MB of memory in use
> Info: Finished startup at 8.06162 s, 133.126 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.
>
>
>
> If the colvar module in the conf file is commented out, ramd runs fine
> and the final pdb (coor) file is also obtained. Conversely, without
> ramd, colvars run fine. It seems to be a matter for developers unless
> (hopefully) it is simply mishandling from my side. Attached hehe
> please find the whole conf file (with colvars commented out), which is
> where errors from my side could be detected.
>
> # 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 15343
> numsteps 100
>
>
> thanks
> francesco
>
>
> On Mon, Mar 28, 2011 at 11:52 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>
>> You only want the tclForce on that's in the ramd.tcl file.  You need to look
>> at the RAMD example since I'm not familiar with how it works.
>>
>> -Jim
>>
>>
>> On Mon, 28 Mar 2011, Francesco Pietra wrote:
>>
>>> On Mon, Mar 28, 2011 at 9:33 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>>>
>>>> It looks like you have "tclForces on" after run or minimize in your
>>>> config
>>>> file, so possibly your tclForces script was not active during the RAMD
>>>> run
>>>> at all.
>>>
>>> Hi  Jim:
>>> Yes, "tclforces on" is in the sourced ramd script, which comes after
>>> the "run" command in namd conf file.  I had checked that against namd
>>> 2.7 with external namd: there was the same order of statements.
>>>
>>> Now, if "tclforces on" is located in namd conf file, at the top:
>>>
>>>
>>> # forcefield
>>> paratypecharmm on
>>> parameters ./par_all27_prot_lipid.prm
>>> parameters ./AP1.r.prm
>>> tclForces on
>>>
>>> the error is:
>>>
>>> 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.
>>> ERROR: 'tclForcesScript' is a required configuration option
>>> ERROR:   when 'tclForces' is set
>>> ERROR: tclForcesScript defines:   Tcl script for global forces
>>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>>
>>>
>>>
>>> Where should "tclforces on" be now located?
>>>
>>> thanks
>>> francesco
>>>
>>>
>>>
>>>>
>>>> -Jim
>>>>
>>>> On Mon, 28 Mar 2011, Francesco Pietra wrote:
>>>>
>>>>> Hi:
>>>>> I carried out a trial RAMD simulation with namd.2.8 (from binary
>>>>> Linux64) charmmff for a protein-organic-ligand in a lipidic membrane.
>>>>>
>>>>> The simulation ended correctly at the bare 100 chosen steps, the
>>>>> ligand did not move - as expected from 1000 steps  acc 0.3 ts 1fs.
>>>>> Everything seems OK except the error below. I vaguely remember that
>>>>> Vlad warned me in the past to compile namd in order that ramd exists
>>>>> correctly. Was that the same errior message or anything new about
>>>>> which I should now care?
>>>>>
>>>>> thanks
>>>>> francesco pietra
>>>>>
>>>>> **************************
>>>>>
>>>>> ENERGY:    1000     10573.6218     17958.2104      9301.2411
>>>>> 779.3272        -763083.0117     55270.6864         0.0000
>>>>> 1.9652    144208.1552        -524989.8044       308.8680
>>>>> -669197.9596   -524727.0908       309.0692           -173.1971
>>>>> -32.1881   2166358.3052       -35.4825       -31.7813
>>>>>
>>>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
>>>>> WRITING COORDINATES TO DCD FILE AT STEP 1000
>>>>> WRITING COORDINATES TO RESTART FILE AT STEP 1000
>>>>> FINISHED WRITING RESTART COORDINATES
>>>>> The last position output (seq=1000) takes 0.134 seconds, 744.610 MB of
>>>>> memory in use
>>>>> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
>>>>> FINISHED WRITING RESTART VELOCITIES
>>>>> The last velocity output (seq=1000) takes 0.021 seconds, 744.609 MB of
>>>>> memory in use
>>>>> TCL: Setting parameter TclForces to on
>>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>> ------------- Processor 1 Exiting: Called CmiAbort ------------
>>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>>
>>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>> ------------- Processor 3 Exiting: Called CmiAbort ------------
>>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>>
>>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>>
>>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>>
>>>>> ------------- Processor 2 Exiting: Called CmiAbort ------------
>>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>> **************************
>>>>>
>>>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:49 CST