Re: Definition of two colvars for ABF

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Jan 05 2010 - 08:12:47 CST

Keeping the mailing list in CC, since others might have ideas about
what is happening. At this point, I don't, unfortunately.

2010/1/5 Branko <bdrakuli_at_chem.bg.ac.yu>:
> Dear Jerome,
>
> Thank you very much for the answer.For windows  execute abf_integrate, I'll
> must ask colleagues skilled in programming, but I try to reproduce (short)
> simulation using just one colvar for simplicity, and using the low
> colvarsRestartFrequency 100 in place of 10000, but <files>.state still did
> not appears. In namd out file, again there is data that those files should
> be generated (please see bellow, underlined0. If this can be helpful part of
> colvar definition file:
>
> colvarsTrajFrequency    1  (same as in previous simulations)
> colvarsRestartFrequency 100 (lower)
> analysis    on (same as in previous simulations)
>
> from NAMD input:
>
> restartfreq         1000  (same as in previous simulations)
>
> and from NAMD output (part that repeat in every iteration, i.e. recorded
> step):
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 24000
> WRITING COORDINATES TO DCD FILE AT STEP 24000
> WRITING COORDINATES TO RESTART FILE AT STEP 24000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 24000
> FINISHED WRITING RESTART VELOCITIES
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> colvars: Synchronizing trajectory file.
> ENERGY:   25000      1774.3401      2569.9087       590.3621
> 0.0705            340.3763     -2520.7006         0.0000         0.0000
> 5115.0868           7869.4439       305.2329      2754.3571
> 7919.9032       309.9006             66.6905       168.5968
> 120000.0000       -75.6140       -75.9222
>
> This "colvars: Synchronizing trajectory file" didn't appear if
> colvarsRestartFrequency is 10000.
> Hope that this could be helpful.
>
> Sincerely
>
> Branko
>
>
>
>
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 29-09-2008.
> colvars: # colvarsTrajFrequency = 1
> colvars: # colvarsRestartFrequency = 100
> 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: Collective variables initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars:   Initializing a new "abf" instance.
> colvars:   # name = "abf1" [default]
> colvars:   # colvars = { d }
> 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:   Finished ABF setup.
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables biases initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module initialized.
> colvars:
> ----------------------------------------------------------------------
>
>
>
>
> Jérôme Hénin wrote:
>
> Dear Branko,
>
> So far, to use abf_integrate under windows, you need to compile it
> yourself (the source files are in the lib/ directory of the NAMD
> source distribution). I have no experience in windows programming, so
> I can't really help you with that.
>
> The lack of a colvars.state file sounds like a problem. What happens
> if you set a fairly low colvarsRestartFrequency?
>
> Best,
> Jerome
>
>
> 2010/1/1 Branko <bdrakuli_at_chem.bg.ac.yu>:
>
>
> 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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