Re: no output for corrfunc

From: Rui Zhang (zhangrui1002_at_gmail.com)
Date: Fri Aug 03 2012 - 10:30:49 CDT

Hi Giacomo,
It was run for 10,000 steps. And the colvars configuration file is:

colvarsTrajFrequency 100
colvarsRestartFrequency 10000

colvar {
name BaseDist

distance {
           group1 {
               atomnumbers { 21 27 28 }
}
           group2 {
               atomnumbers { 59746 59747 59749 }
}
}
corrfunc on
corrfunctype coordinate
corrfunclength 1000
}

colvar {
name LysCoorNum

distance {
           group1 {
               atomnumbers { 27 }
}
           group2 {
               atomnumbers { 9831 }
}
}
corrfunc on
corrfunctype coordinate
corrfunclength 1000
}

analysis on

Thank you!
Rui

On Thu, Aug 2, 2012 at 6:15 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> Hello Rui, can you send the number of simulation steps, or even better the
> other configuration files? You can send them off list if you prefer.
>
> Giacomo
>
>
> On Thu, Aug 2, 2012 at 8:06 PM, Rui Zhang <zhangrui1002_at_gmail.com> wrote:
>
>> Hi,
>> I was trying to calculation the auto-correlation function for a colvar.
>> But the corrfunc.dat file was produced even though the calculation was
>> finished successfully. And the output showed:
>>
>> colvars: Initializing a new collective variable.
>> colvars: # name = Lysdist
>> colvars: Initializing a new "distance" component.
>> colvars: # componentCoeff = 1 [default]
>> colvars: # componentExp = 1 [default]
>> colvars: # period = 0 [default]
>> colvars: # wrapAround = 0 [default]
>> colvars: # forceNoPBC = off [default]
>> colvars: # oneSiteSystemForce = off [default]
>> colvars: Initializing atom group "group1".
>> colvars: Atom group "group1" defined, 1 initialized: total mass =
>> 15.9994.
>> colvars: Initializing atom group "group2".
>> colvars: Atom group "group2" defined, 1 initialized: total mass =
>> 14.007.
>> colvars: All components initialized.
>> colvars: # width = 1 [default]
>> colvars: # lowerBoundary = 0 [default]
>> colvars: # lowerWallConstant = 0 [default]
>> colvars: # upperBoundary = 0 [default]
>> colvars: # upperWallConstant = 0 [default]
>> colvars: # expandBoundaries = off [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 = on
>> colvars: # corrFuncWithColvar = "Lysdist" [default]
>> colvars: Calculating auto-correlation function.
>> colvars: # corrFuncType = coordinate
>> colvars: # corrFuncOffset = 0 [default]
>> colvars: # corrFuncLength = 1000
>> colvars: # corrFuncStride = 1 [default]
>> colvars: # corrFuncNormalize = on [default]
>> colvars: # corrFuncOutputFile = "stats2.Lysdist.corrfunc.dat" [default]
>>
>> Could you help me check why there's no output for corrfunc? Thank you!
>>
>> Rui
>>
>
>

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