Re: Definition of two colvars for ABF

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Tue Jan 05 2010 - 08:19:14 CST

Sorry,

I received two identical messages (one from your address the other from
namd-l) so I simply replay on the one of those messages.

Sincerely

Branko

Jérôme Hénin wrote:
> 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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