From: Ferenc Ötvös, PhD (otvos_at_brc.hu)
Date: Fri Mar 26 2010 - 04:45:27 CDT
Dear Members,
Possibly I am not using the colvar module the right way, but I am not
able to use the colvar functionality in NAMD 2.7b2.
The system has 4 segments, of witch 4 atoms (1 from each segment)
would be restrained by a dihedral angle. It did not work either in
autoimd session or in a background run.
I should be very grateful if someone could help me with this issue.
Thanks
Ferenc Otvos
Some details that may be essential follows below:
NAMD config file:
set paramfile_list {par_all27_prot_lipid_na.inp}
set imdport 6150
set sim_mode equilibrate
set namdoutputrate 1
set dcdfreq 0
set temperature 300
set minimizesteps 100
set runsteps 1000000
set MYSCRIPT {}
##############################################################3
##
## This file is used as a template for running NAMD jobs
## When this file is run, the following Tcl variables will
## have been initialized to appropriate values:
## imdport, minimizesteps, runsteps, paramfile_list
##
###############################################################3
# Input
structure autoimd.psf
coordinates autoimd.pdb
paraTypeCharmm on
foreach paramfile $paramfile_list {
parameters $paramfile
}
temperature $temperature
# Output
if { $dcdfreq > 0 } {
DCDFile autoimd.dcd
DCDFreq $dcdfreq
}
# IMD parameters
imdon on
imdport $imdport
imdfreq $namdoutputrate
imdwait on
# Fixed Atoms
fixedAtoms on
fixedAtomsFile autoimd.pdb
fixedAtomsCol B
# Collective variables section
colvars on
colvarsConfig colvars.config
# Integrator and dynamics parameters
rigidbonds all
timestep 2.0
nonBondedFreq 1
stepsPerCycle 10
switching on
switchDist 10
cutoff 12
pairlistdist 14
exclude scaled1-4
1-4scaling 1.0
langevin on
langevinDamping 3
langevinTemp $temperature
langevinHydrogen no
# Output options
outputname autoimd_out
outputTiming 1000
eval $MYSCRIPT
# This line permits AutoIMD to connect to jobs running on remote machines
print "AUTOIMD HOST: [info hostname] PID: [pid]"
# Run simulation
minimize $minimizesteps
reinitvels $temperature
run $runsteps
colvar config file:
# collective variables config file: dihedrals
colvarsTrajFrequency 100 # output values every 100 steps
colvarsRestartFrequency 10000
analysis on
colvar {
name dihedral1 # needed to identify the variable
outputSystemForce no # report also the system force on this colvar
# (in addition to the current value)
dihedral {
group1 {
atomNumbers 5
}
group2 {
atomNumbers 1921
}
group3 {
atomNumbers 3837
}
group4 {
atomNumbers 5753
}
}
}
harmonic {
name torsions
colvars {
dihedral1
}
centers {
0.0
}
forceConstant 5
}
Part of the log file:
Info: STRUCTURE SUMMARY:
Info: 7665 ATOMS
Info: 7740 BONDS
Info: 14000 ANGLES
Info: 20436 DIHEDRALS
Info: 1176 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 0 FIXED ATOMS
Info: 3864 RIGID BONDS
Info: 0 RIGID BONDS BETWEEN FIXED ATOMS
Info: 19131 DEGREES OF FREEDOM
Info: 3801 HYDROGEN GROUPS
Info: 0 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 54223.9 amu
Info: TOTAL CHARGE = -6 e
Info: *****************************
Info:
Info: Entering startup at 348502 s, 3.82005 MB of memory in use
Info: Startup phase 0 took 0.00030351 s, 3.82006 MB of memory in use
Info: Startup phase 1 took 0.0280507 s, 5.72552 MB of memory in use
Info: Startup phase 2 took 0.000191086 s, 5.78677 MB of memory in use
Info: PATCH GRID IS 3 BY 3 BY 4
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.0507798 -0.037221 -0.0543319
Info: LARGEST PATCH (12) HAS 573 ATOMS
Info: CREATING 487 COMPUTE OBJECTS
Info: Startup phase 3 took 0.0231574 s, 6.77894 MB of memory in use
Info: Startup phase 4 took 0.000164252 s, 6.77883 MB of memory in use
Info: Startup phase 5 took 0.000162553 s, 6.77872 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 0.000234515 s, 6.77962 MB of memory in use
Info: CREATING 487 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.44089e-16 AT 0.121031
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04097e-13 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
Info: Interactive MD listening on port 6150.
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 20090807.
colvars: # analysis = on
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 10000
colvars: The trajectory file will be "autoimd_out.colvars.traj".
colvars: The final output state file will be "autoimd_out.colvars.state".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = dihedral1
colvars: Initializing a new "dihedral" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass
= 12.011.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass
= 12.011.
colvars: Initializing atom group "group3".
colvars: Atom group "group3" defined, 1 initialized: total mass
= 12.011.
colvars: Initializing atom group "group4".
colvars: Atom group "group4" defined, 1 initialized: total mass
= 12.011.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off
colvars: # outputAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = torsions
colvars: # colvars = { dihedral1 }
colvars: # forceConstant = 5
colvars: # centers = { 0 }
colvars: # targets = { 0 } [default]
colvars: # forceConstantTarget = 0 [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
Info: Startup phase 7 took 0.0179073 s, 9.07521 MB of memory in use
Info: Startup phase 8 took 0.000470199 s, 13.7061 MB of memory in use
Info: Finished startup at 348502 s, 13.7061 MB of memory in use
TCL: Minimizing for 100 steps
Info: INTERACTIVE MD AWAITING CONNECTION
Info: IMD connection opened
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG
ENERGY: 0 326.9165 8396.1314 2375.9181
12.6324 -1438.2852 1390925468.8494 0.0000
0.0000 0.0000 1390935142.1626 0.0000
1390935142.1626 1390935142.1626 0.0000
MINIMIZER SLOWLY MOVING 14 ATOMS WITH BAD CONTACTS DOWNHILL
colvars: Error: cannot find the total force of atom 5. Is energy
minimization (instead of MD) enabled?
colvars: If this error message is unclear, try recompile with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
Charm++ fatal error:
FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0] _ZN12colvarmodule11fatal_errorERKSs+0xf [0x83bcca1]
[1] _ZThn8_N16colvarproxy_namd9calculateEv+0xd [0x844a5c1]
[2] _ZN18GlobalMasterServer11callClientsEv+0x42f [0x83a6563]
[3] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x5ec
[0x83a5c0c]
--------------------------------------------------
I tried couple of different variations in configs, but the key error
was all the time:
colvars: Error: cannot find the total force of atom 5......
Ferenc Otvos, PhD
Institute of Biochemistry
Biological Research Center, Szeged, Hungary
Temesvari krt. 62, Szeged, Hungary, H-6726
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