MD simulation doesn't run very long

andrew...@eas.gatech.edu ast... at gmail.com
Fri Feb 1 21:28:44 CET 2008


Ciao Teo,

Well hmmm.  We had tried running the simulation on mpp2 at EMSL using
another version of cp2k and that gave us the same error.  I think that
version was compiled with pgi -- but we were also using the binary in
someone else's directory so there could have been libraries that got
their links messed up.

I have read about the issues with gfortran.  I used it anyway because
that was the only thing I could even get cp2k to compile with!  :)
I'll try it again with g95.

Thanks a lot for your help and running the file for me!!

Cheers,
Andrew


On Feb 1, 2:11 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> Ciao Andrew,
>
> > lammps but cp2k ran into some connectivity issues (cp2k doesn't seem
> > to find water molecules automatically across cell boundaries).  I
>
> this is not the case.. cp2k uses PBC also to identify the connectivity..
> The point could be that water is a little bit tricky.. if the
> geometry is a little bit distorted with hydrogen bonds is
> anyway difficult to identify a proper water molecule as an
> independent unity..
> That's why is always better in my opinion to use an external topology
> file as you did after..
>
> > fixed this, by making certain the water molecules were all in the
> > image reference and defining the connectivity manually.  This didn't
> > fix that specific problem though: the symptom is that the simulation
> > runs for ~20-30 time steps and then the temperature increases
> > dramatically and we get some atoms crash:
>
> I was running your input file for several time steps (see the
> attached output file) and I don't get
> any error..
> I suppose gfortran is miscompiling cp2k (and I would not be
> surprised.. as far as I know only very recent version of gfortran
> can compile cp2k)..
>
> I would suggest you to use g95 (if you want to go for a free
> compiler) or intel.
>
> I'm sorry but as you may have already read on this group cp2k is
> quite demanding in terms of fortran compilers..
> Hope this helps!
> Teo
>
>  out.gz
> 73KDownload
>
>
>
>
>
> > **********************************************************************
> > *********
> >  ENSEMBLE TYPE
> > =                                              nvt
> >  STEP NUMBER
> > =                                               26
> >  TIME [FS]                    =
> > 26.000000
> >  CONSERVED QNTY               =
> > -0.299834451059E+01
>
> >                                          INSTANTANEOUS        AVERAGES
> >  CPU [S]                      =
> > 0.22                 0.39
> >  {E-E0}/{k_b*N_at}            =          0.396202120408E+02
> > 0.335570376311E+01
> >  POTENTIAL ENERGY[hartree]    =         -0.549743589253E+01
> > -0.462863744377E+01
> >  KINETIC ENERGY[hartree]      =          0.249463138359E+01
> > 0.153631845774E+01
> >  TEMPERATURE[K]               =
> > 656.451              404.275
>
> > **********************************************************************
> > *********
>
> >  WARNING| Particles:     609    265 at distance [au]:     0.49549362
> > less than:      0.95400000; increase EMAX_SPLINE.
>
> > The temperature was supposed to be 300 K, but as you can see it blows
> > up the last few time steps.
>
> > Here is a link to the files:
> >http://shadow.eas.gatech.edu/~astack/water.tar.gz
>
> > Here is my input file, the commented out sections are different things
> > we tried to see if that made a difference.  The biggest thing that
> > seemed to affect the number of time steps was the options affecting
> > the spline.
>
> > &FORCE_EVAL
> >   METHOD FIST
> >   &MM
> >     &FORCEFIELD
> > !       &SPLINE
> > !               EMAX_SPLINE 1000.0
> > !               R0_NB [angstrom] 0.1
> > !       &END SPLINE
> >       &BEND
> >          ATOMS H O H
> >          KIND HARMONIC
> >          K [kcalmol*rad^-2] 120
> >          THETA0 [deg] 109.47
> >        &END BEND
> >        &BOND
> >          ATOMS O H
> >          KIND HARMONIC
> >          K [kcalmol*angstrom^-2] 500
> >          R0 [angstrom] 1.00
> >        &END BOND
> >       &NONBONDED
> >         &LENNARD-JONES
> >            ATOMS O O
> >            EPSILON [kcalmol] 0.1848
> > !           SIGMA [angstrom] 3.5532
> >            SIGMA [angstrom] 3.1655
> >            RCUT [angstrom] 10.0
> >          &END LENNARD-JONES
> >          &LENNARD-JONES
> >            ATOMS O H
> >            EPSILON [kcalmol] 0.0430
> > !           SIGMA [angstrom] 1.7883
> >            SIGMA [angstrom] 1.5932
> >            RCUT [angstrom] 10.0
> >          &END LENNARD-JONES
> >          &LENNARD-JONES
> >            ATOMS H H
> >            EPSILON [kcalmol] 0.0100
> > !           SIGMA [angstrom] 0.900
> >            SIGMA [angstrom] 0.8018
> >            RCUT [angstrom] 10.0
> >          &END LENNARD-JONES
> >       &END NONBONDED
> >     &END FORCEFIELD
> >     &POISSON
> >       &EWALD
> >         EWALD_TYPE ewald
> >         ALPHA 0.5
> >         GMAX 15
> >       &END EWALD
> >     &END POISSON
> >   &END MM
> >   &SUBSYS
> >     &CELL
> >       ABC 20 20 20
> >       UNIT ANGSTROM
> >       PERIODIC XYZ
> >     &END CELL
> >     &TOPOLOGY
> >         CONN_FILE_NAME water.psf
> >         CONNECTIVITY UPSF
> >         COORD_FILE_NAME water.pdb
> >         COORDINATE PDB
> >     &END TOPOLOGY
> >     &PRINT
> >       &TOPOLOGY_INFO HIGH
> >         FILENAME topology.inf
> >         PDB_INFO
> >         COMMON_ITERATION_LEVELS 1
> >         UTIL_INFO
> >         GENERATE_INFO
> >       &END TOPOLOGY_INFO
> >     &END PRINT
> >   &END SUBSYS
> > !  &RESCALE_FORCES
> > !    MAX_FORCE 0.001
> > !  &END
> > !  &PRINT
> > !       &FORCES
> > !         FILENAME water.force
> > !        &END FORCES
> > !  &END PRINT
> > &END FORCE_EVAL
> > &GLOBAL
> >   PROJECT water
> >   RUN_TYPE MD
> > !  PRINT_LEVEL HIGH
> > &END GLOBAL
> > &MOTION
> >   &MD
> >     ENSEMBLE NVT
> >     STEPS 300
> >     TIMESTEP 1
> >     TEMPERATURE 300
> > !    TEMP_TOL 1.0
> >    &THERMOSTAT
> >     &NOSE
> >       LENGTH 1
> >       YOSHIDA 3
> >       MTS 2
> >       TIMECON 500
> >     &END NOSE
> >    &END THERMOSTAT
> >    &PRINT
> >     &ENERGY HIGH
> >      EACH 1
> >     &END ENERGY
> >    &END PRINT
> >   &END MD
> > &END MOTION
>
> > 



More information about the CP2K-user mailing list