Re: Restarting ABF

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Thu Aug 13 2009 - 16:00:20 CDT

Hi Branko, did you complete successfully the NAMD simulation, of which
you're pasting the output?

If you did, and the colvars output files (whose names you underlined)
had not been created, that would mean a serious bug on the Windows
architecture (which I assume you're using).

Can you confirm that NAMD exited successfully but "forgot" to write
among other things the colvars state file? If you saw the line "End
of program" but NOT the following line:
colvars: Saving collective variables state to
"C:\namd2\24diMeinthd.colvars.state".
that would be the case.

Thanks in advance for any more detailed information you can provide.

Giacomo

---- ----
 Giacomo Fiorin
   ICMS - Institute for Computational Molecular Science
     Temple University
     1900 N 12 th Street, Philadelphia, PA 19122
 work phone: (+1)-215-204-4216
 mobile: (+1)-267-324-7676
 mail: giacomo.fiorin_<at>_gmail.com
---- ----

On Thu, Aug 13, 2009 at 2:56 PM, Branko<bdrakuli_at_chem.bg.ac.yu> wrote:
> Hi Jerome, Cris,
>
> Thank you very much for prompt respond. But, during previous part of
> simulation colvars restart files were not generated. Part of ~ beginning of
> initial simulation.out file and colvars configuration are added below,
> please let me know where I should made change(s) in configuration to
> overcome similar situation in future. Thanks a lot.
>
> Sincerely
>
> Branko
>
> If you have time, please explain in brief function of "trajAppend". Thanks
>
> NAMD.out:
> 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\24diMeinthd.restart.colvars.state".
> colvars: The trajectory file will be "C:\namd2\24diMeinthd.colvars.traj".
> colvars: The final output state file will be
> "C:\namd2\24diMeinthd.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 = 3.36
> colvars: Lower boundary defined.
> colvars: # upperBoundary = 9.73
> 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.
>
>
> Jerome Henin wrote:
>
> Hi Branko,
>
> As with any colvars simulation, restarting is done using the
> colvarsInput keyword, followed by the name of the colvars state file
> for the previous run. The following is then written to standard output
> at the end of the colvars startup:
>
> colvars: Restarting from file "r34-abf00.colvars.state".
> colvars: Restarting collective variable "ra" from value: 1.80515
> colvars: Restarting collective variable "r310" from value: 4.16205
> colvars: Restarting collective variable "ro" from value: 4.24923
> colvars: Restarting ABF bias "abf1".
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module initialized.
> colvars:
> ----------------------------------------------------------------------
>
>
> Colvars configuration:
> colvarsTrajFrequency 1
> colvarsRestartFrequency 10000
> analysis on
>
>
> colvar {
>
> name d
>
> lowerBoundary 3.36
> upperBoundary 9.73
> width 0.01
>
> distance {
> group1 {
> atomnumbers 1 3 5
> }
> group2 {
> atomnumbers 16 17 18
> }
> }
> }
>
> abf {
> colvars d
> fullSamples 500
> hideJacobian no
> outputFreq 1000
> applyBias yes
> }
>
>
> Best,
> Jerome
>
> On Thu, Aug 13, 2009 at 12:05 PM, Branko<bdrakuli_at_chem.bg.ac.yu> wrote:
>
>
> Hi to all,
>
> Is there any way to continue with abf calculation (of any type) after
> restarting of MD (which is trivial). On the other words, can output from
> previous ABF calculation can be in some way added to continuation of same
> MD simulation.
> Every advise is highly appreciated.
>
> Branko
>
>
>
>
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