Coordination number CV

Martin martin.m... at gmail.com
Wed Feb 20 17:50:41 CET 2013


Hi all,

I am using coordination number as a collective variable in a metadynamics 
simulation in CP2K.  I have read already that cp2k normalizes the 
coordination number by the number of atoms thus it should always be between 
0 and 1.  I am concerned that there is a bug because I get values slightly 
higher than 1 (e.g. 1.20021749) in my COLVAR.dat file as well as in my free 
energy output.  Does anybody know why this might be happening?

Thanks.
Martin

Here are the pertinent parts of my input file:

 &GLOBAL
   PREFERRED_FFT_LIBRARY  FFTSG
   EXTENDED_FFT_LENGTHS  T
   PRINT_LEVEL  MEDIUM
   PROJECT_NAME GACTIN
   RUN_TYPE  MD
 &END GLOBAL
 &MOTION
   &MD
     ENSEMBLE  NVT
     STEPS  10000
     TIMESTEP     4.9999999999999989E-01
     STEP_START_VAL  10531
     TIME_START_VAL     5.5554999999993852E+03
     ECONS_START_VAL    -1.3825824210408957E+03
     TEMPERATURE     3.1000000000000000E+02
     COMVEL_TOL     1.0000000000000001E-05
     &THERMOSTAT
       TYPE  NOSE
       &NOSE
         TIMECON     9.9999999999999964E+00
         &COORD
              -1.9870307101421267E+00    1.5164403362900575E+02   
 2.0651877984243871E+04
         &END COORD
         &VELOCITY
              -2.6525573239549802E-06    1.6855266002596401E-03   
 3.2669753771567196E-03
         &END VELOCITY
         &MASS
               1.9734082808800943E+07    1.6778542540323039E+02   
 1.6778542540323039E+02
         &END MASS
         &FORCE
              -1.0987144495918850E-08   -5.0234551461375742E-06   
-3.0100014648276899E-06
         &END FORCE
       &END NOSE
     &END THERMOSTAT
  &END MD
  &FREE_ENERGY
     METHOD  METADYN
     &METADYN
       TEMPERATURE     3.1000000000000000E+02
       MIN_DISP     2.9999999999999999E-02
       OLD_HILL_NUMBER  649
       OLD_HILL_STEP  6925
       TEMP_TOL     2.0000000000000003E+02
       WW     1.9599999999999999E-03
       DO_HILLS  T
       DELTA_T     2.4000000000000000E+03
       LAGRANGE  T
       STEP_START_VAL  6931
       NHILLS_START_VAL  649
       COLVAR_AVG_TEMPERATURE_RESTART     3.4475790517869569E+02
       &METAVAR
         LAMBDA     2.0000000000000000E+00
         MASS     4.9999999999999972E+01
         SCALE     2.0000000000000000E-02
         COLVAR  1
       &END METAVAR
       &METAVAR
         LAMBDA     2.0000000000000000E+00
         MASS     4.9999999999999972E+01
         SCALE     2.0000000000000000E-02
         COLVAR  2
       &END METAVAR
       &PRINT
         &COLVAR  SILENT
           FILENAME =COLVAR.dat
           &EACH
             MD  1
           &END EACH
         &END COLVAR
         &HILLS  SILENT
           FILENAME =HILLS.dat
           &EACH
             MD  1
           &END EACH
         &END HILLS
       &END PRINT
     &END METADYN
   &END FREE_ENERGY
 &END MOTION

....
 &FORCE_EVAL
   &SUBSYS
   ....
     &COLVAR
       &COORDINATION
         ATOMS_FROM  5871
         ATOMS_TO  5870 5868 5869
         R0     4.5000000000000000E+00
       &END COORDINATION
     &END COLVAR
     &COLVAR
       &COORDINATION
         ATOMS_FROM  5871
         ATOMS_TO  5876 5879 5882 5885 5888 5894 5897 5939 6533 \
          10418 12167 15677 16733 19781 23543 23597 24299 24314 25400 \
          29297 34814 39116 39695 44897 50948 53462 55361
         R0     4.5000000000000000E+00
       &END COORDINATION
     &END COLVAR
   ....
   &END SUBSYS
 &END FORCE_EVAL
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