Re: Fwd: Incompatibility between colvars and tclforces?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 31 2011 - 02:45:10 CDT

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: J√©r√īme H√©nin<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, J√©r√īme H√©nin<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, J√©r√īme H√©nin<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