From: Rui Zhang (zhangrui1002_at_gmail.com)
Date: Fri Aug 03 2012 - 16:28:35 CDT
I tried it just now, but it didn't give any corrfunc.dat file...
Rui
On Fri, Aug 3, 2012 at 3:01 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> 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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