Re: no output for corrfunc

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Aug 03 2012 - 16:01:59 CDT

Have you tried using "numsteps $nSteps"?
On Aug 3, 2012 4:53 PM, "Rui Zhang" <zhangrui1002_at_gmail.com> wrote:

> Hi Giacomo,
> The namd configuration file concerning the number of steps is below.
>
> PME on ;# use PME electrostatics
> PMEGridSizeX 149 ;# use 147 grid points along
> cellbasisVector1
> PMEGridSizeY 165 ;# use 165 grid points along
> cellbasisVector2
> PMEGridSizeZ 150 ;# use 152 grid points along
> cellbasisVector3
>
> # ABF SECTION
>
> colvars on
> colvarsConfig rxn1.in
>
> outputname $outputname ;# output files with this filename
> restartfreq 200 ;# generate a restart file every
> 500 fs
> dcdfreq 1000 ;# write a new dcd file every 500
> fs
> outputEnergies 1000 ;# output energy every 100 fs
> outputPressure 1000 ;# output pressure every 100 fs
> outputTiming 1000 ;# output timing every 100 fs
>
>
> set nSteps 10000
>
> run $nSteps
>
> Thank you!
> Rui
>
> On Fri, Aug 3, 2012 at 2:16 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
>
>> Hello Rui, I need also the NAMD configuration file, because "run 10000"
>> is not exactly the same as "numsteps 10000".
>>
>> Thanks
>> Giacomo
>>
>>
>> On Fri, Aug 3, 2012 at 11:30 AM, Rui Zhang <zhangrui1002_at_gmail.com>wrote:
>>
>>> 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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