From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Nov 25 2014 - 05:11:55 CST
Dear Kanchi,
Thanks and it works.
However I am then facing problems of unstable simulation.
ERROR: Atom 307885 velocity is 45034.5 16158 17327.8 (limit is 6000,
atom 643 of 645 on patch 0 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms
on patch 0 pe 0).
ERROR: Constraint failure in RATTLE algorithm for atom 108888!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 103029!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atom 213425 velocity is 8088.22 -1869.58 -14038.8 (limit is
6000, atom 322 of 653 on patch 39 pe 0)
ERROR: Atom 213426 velocity is 8040.03 -1902.73 -14210.9 (limit is
6000, atom 323 of 653 on patch 39 pe 0)
ERROR: Atom 213427 velocity is 7928.5 -1868.46 -14058.3 (limit is
6000, atom 324 of 653 on patch 39 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (3 atoms
on patch 39 pe 0).
ERROR: Constraint failure in RATTLE algorithm for atom 26019!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 32074!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 27715!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
I have changed the force constant to other values (bigger or smaller).
I am not sure whether the problem orienting from the force constant or
other simulation parameters. The main parameter comes from the
previous MD simulations for the system which has run for hundreds of
ns.
Regards,
Kevin
On Tue, Nov 25, 2014 at 4:08 PM, Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:
> Hi Kevin,
> I hope try the fallowing and let us know if you end with same
> error.
>
> harmonic {
> colvars ProjectionZ
> centers 40.0
> forceConstant 4.0
> targetCenters 40.0
> targetNumSteps 1
> }
>
>
> cheers,
> Subbarao Kanchi
>
>
> On Tue, Nov 25, 2014 at 11:40 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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