Re: Incompatibility between colvars and tclforces?

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Wed Mar 30 2011 - 11:20:08 CDT

Hello Francesco, you mentioned running on a "small machine" to repeat the
test. Where did you run the job the first time? Was tclForces supported in
that NAMD version? It used to be that on certain machines compiling NAMD
with Tcl support required too much extra work, and Tcl was left out.
Luckily, this is not the case any more, most of the time. But I wonder if
you were in such a situation.

Also, which was the NAMD version installed on the "bigger machine"? 2.8b1
or earlier?

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Wed, Mar 30, 2011 at 10:06 AM, 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--0016e6471800a81e76049fb58e82--

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