From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Tue Nov 25 2014 - 06:30:36 CST
It is compiling bad contact. Try with 1fs time step with out constraint
hydrogen bonds. It suppose to work. I am also getting same problem with
time step 2fs.
Cheers
Subbarao Kanchi
On 25 Nov 2014 16:41, "Kevin C Chan" <cchan2242-c_at_my.cityu.edu.hk> wrote:
> 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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