From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Mar 31 2011 - 05:12:10 CDT
Francesco,
What happens to the ligand while applying the RAMD when the energies
blow up ?
Does it remain at its place or it moves away ?
Are the colvars restraints still satisfied when you apply RAMD ?
It also looks to me like a physical problem with your system right now
instead of an implementation problem ...
That's why I kept on suggesting to try a test case like the NAMD
tutorials ... Take the system from the tcl forces tutorial, apply
colvars to restrain some part of the system (on which tcl forces will
not be applied) and then run the tcl forces tutorial (which is a
constant velocity pulling) ... You can also take our RAMD example and
before running it, apply colvars to restrain some arbitrary distances
(check where the ligand goes out in a test without colvars and choose
distances for colvars restraints that are far away from any residue
involved in ligand egress).
I have not used colvars thus far, although I will use it soon ... If
you make a test simulation (either from the tcl forces tutorial or from
our RAMD example) and you can reproduce the problem I can also offer to
test it ...
Vlad
On 03/31/2011 09:45 AM, Francesco Pietra wrote:
> Vlad:
> As I wrote before, the system was npt equilibrated with colvars.
> Finely equilibrated, that is, energies in order. I also checked that
> the distances set in colvars were maintained. It seems that ramd is a
> special type of tclforces but I am confident that the house will be
> put in order by the experts.
>
> francesco
>
> On Thu, Mar 31, 2011 at 9:27 AM, Vlad Cojocaru
> <vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
>> 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
>>
>>
>>
-- 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 : Wed Feb 29 2012 - 15:56:53 CST