Re: Restarting ABF

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Thu Aug 13 2009 - 13:56:59 CDT

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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