From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Nov 25 2014 - 21:11:41 CST
Thanks for all the replies,
I have solved the problem by disabling
useGroupPressure
useFlexibleCell
useConstantRatio
I guess they are not suitable for a run with colvars. Also I kept a
timestep of 2 fs.
Regards,
Kevin
On Tue, Nov 25, 2014 at 10:53 PM, Giacomo Fiorin
<giacomo.fiorin_at_gmail.com> wrote:
> Please read the entire output, including the 2 lines before the last.
>
> On Nov 25, 2014 1:10 AM, "Kevin C Chan" <cchan2242-c_at_my.cityu.edu.hk> wrote:
>>
>> Dear Users,
>>
>> I just ran into an issue with colvars parameters,
>>
>> colvars:
>> ----------------------------------------------------------------------
>> colvars: Collective variables initialized, 1 in total.
>> colvars:
>> ----------------------------------------------------------------------
>> colvars: Initializing a new "harmonic" instance.
>> colvars: # name = "harmonic1" [default]
>> colvars: # colvars = { ProjectionZ }
>> colvars: # outputEnergy = off [default]
>> colvars: # forceConstant = 5
>> colvars: The force constant for colvar "ProjectionZ" will be rescaled to
>> 20 according to the specified width.
>> colvars: # centers = { 40 }
>> colvars: # targetCenters = { 40 } [default]
>> colvars: # targetForceConstant = 0 [default]
>> colvars: # outputCenters = on
>> colvars: # outputAccumulatedWork = on
>> colvars: Tried to initialize a grid on a variable with undefined
>> boundaries.
>> colvars: If this error message is unclear, try recompiling with
>> -DCOLVARS_DEBUG.
>> FATAL ERROR: Error in the collective variables module: exiting.
>>
>> and the relevant input is:
>>
>> colvar {
>> name ProjectionZ
>>
>> width 0.5
>>
>> distanceZ {
>>
>> main {
>> atomsFile main.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> atomsFile ref.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> }
>> }
>>
>> harmonic {
>> colvars ProjectionZ
>> centers 40
>> forceConstant 5.0
>> outputCenters yes
>> outputAccumulatedWork yes
>> }
>>
>> From the Error message, I have no idea what’s up.
>>
>> Thanks in advance,
>>
>> Kevin
>> ukevi_at_gmx.hk
>>
>
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