Re: Definition of two colvars for ABF

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Fri Jan 01 2010 - 09:58:30 CST

Dear All,

Introducing of boundaries within "gyration colvar" solve the problem and
simulation proceed to the end. Good choice is that one have some
previous simulation of the similar type to estimate boundaries. Now I
appreciate if one could advice me how to made integration. As I use
Win version and abf_integrate exist only under the linux version, I try
to copy whole folder within "lib" directory, but "integrate" or
"abf_integrate" can not be recognized as a command (command prompt with
properly chosen path). Also can VMD console could be helpful?. Thanks in
advance.

Branko

Branko wrote:
> Dear All,
>
> I am trying to define two colvars for ABF (2.7b1 Windows version),
> using configuration given below, all atoms belong to the same molecule
> and atoms in first colvar do not overlapped with the atoms of the
> second one (i.e. are orthogonal). Simulation using the first colvars
> only proceed smoothly, but the second one is likely the problem.
> So the question is are boundaries for "gyration" must be defined, if
> are requisite how to estimate values . As a additional note still I
> can't find colvars.state file during successfully simulation. Best
> wishes to developers and users in New 2010.
>
> Kind regards
>
> Branko
>
> Output (problem underlined):
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 29-09-2008.
> colvars: # colvarsTrajFrequency = 1
> colvars: # colvarsRestartFrequency = 10000
> colvars: # trajAppend = off [default]
> colvars: The restart output state file will be
> "C:\namd2\246triEtinthd.restart.colvars.state".
> colvars: The trajectory file will be
> "C:\namd2\246triEtinthd.colvars.traj".
> colvars: The final output state file will be
> "C:\namd2\246triEtinthd.colvars.state".
> colvars: # analysis = on
> colvars:
> ----------------------------------------------------------------------
> colvars: # readTrajectory = "" [default]
> colvars: # readBegin = 0 [default]
> colvars: # readEnd = 0 [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = d
> colvars: Initializing a new "distance" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # oneSiteSystemForce = off [default]
> colvars: Initializing atom group "group1".
> colvars: Atom group "group1" defined, 3 atoms, total mass = 36.0321.
> colvars: Initializing atom group "group2".
> colvars: Atom group "group2" defined, 3 atoms, total mass = 44.0095.
> colvars: All components initialized.
> colvars: # width = 0.01
> colvars: # lowerBoundary = 3.35
> colvars: Lower boundary defined.
> colvars: # upperBoundary = 9.7
> colvars: Upper boundary defined.
> colvars: # lowerWallConstant = 0 [default]
> colvars: # upperWallConstant = 0 [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # runAve = off [default]
> colvars: # corrFunc = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = gyration
> colvars: Initializing a new "radius of gyration" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: Initializing atom group "atoms".
> colvars: Atom group "atoms" defined, 15 atoms, total mass = 212.181.
> colvars: All components initialized.
> colvars: # width = 0.01
> colvars: # lowerBoundary = 0 [default]
> colvars: Lower boundary was not defined.
> colvars: # upperBoundary = 0 [default]
> colvars: Upper boundary was not defined.
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputSystemForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # runAve = off [default]
> colvars: # corrFunc = off [default]
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables initialized, 2 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing a new "abf" instance.
> colvars: # name = "abf1" [default]
> colvars: # colvars = { d, gyration }
> colvars: # applybias = on
> colvars: # hidejacobian = off
> colvars: Jacobian (geometric) forces will be included in reported
> free energy gradients.
> colvars: # fullsamples = 500
> colvars: # inputprefix = [default]
> colvars: # outputfreq = 1000
> colvars: _Tried to initialize a count grid on variable with
> undefined boundaries._
> colvars: _If this error message is unclear, try recompile with
> -DCOLVARS_DEBUG_.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> Input:
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 10000
> analysis on
>
>
> colvar {
>
> name d
>
> lowerBoundary 3.35
> upperBoundary 9.70
> width 0.01
>
> distance {
> group1 {
> atomnumbers 1 3 5
> }
> group2 {
> atomnumbers 16 17 18
> }
> }
> }
>
> colvar {
> name gyration
> width 0.01
>
> gyration {
> atoms {
> atomNumbers 7 8 9 10 11 12 13 14 15 19 20 21 22 23 24
> }
> }
> }
>
> abf {
> colvars d gyration
> fullSamples 500
> hideJacobian no
> outputFreq 1000
> applyBias yes
> }
> ------------------------------------------------------------------------
>
>
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