Thermostats in QMMM with constraints

shihao shi... at gmail.com
Mon Jan 25 00:32:09 CET 2010


Hi Teo,

Thanks for your reply.  I've done some tests with two water molecules
using Fist and the same error (User Defined thermostats with global
constraints not implemented!) is shown when I use user-defined
thermostat region and intermolecular constraints.  If I remove the
constraint or change the constraint to intramolecular (between atoms 1
and 2), the program works fine. Could you take a look at it?  Thanks a
lot!

Regards,
Shihao


Here's the test input file that gives error:

*******************************************************************
&FORCE_EVAL
  METHOD FIST
  &MM
    &FORCEFIELD
      parm_file_name water.pot
      parmtype CHM
      &CHARGE
        ATOM OT
        CHARGE -0.8476
      &END CHARGE
      &CHARGE
        ATOM HT
        CHARGE 0.4238
      &END CHARGE
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE spme
        ALPHA .44
        GMAX 30
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
    &CELL
      ABC 24.955 24.955 24.955
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME water_2.pdb
      COORDINATE pdb
    &END TOPOLOGY
    &COLVAR
      &DISTANCE
        ATOMS 1 4
      &END
    &END
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT water_1
  RUN_TYPE MD
&END GLOBAL
&MOTION
  &MD
    ENSEMBLE NVT
    STEPS 10
    TIMESTEP 2.5
    TEMPERATURE 298
    &THERMOSTAT
      TYPE                     NOSE
      REGION                   DEFINED
      &NOSE
        LENGTH                 3
        YOSHIDA                3
        TIMECON                100
        MTS                    2
      &END NOSE
      &DEFINE_REGION
        LIST 1 2 3 4 5 6
      &END DEFINE_REGION
    &END THERMOSTAT
    &THERMAL_REGION
      &DEFINE_REGION
        LIST 1 2 3 4 5 6
        TEMPERATURE 298.15
      &END DEFINE_REGION
    &END THERMAL_REGION
  &END MD
  &CONSTRAINT
    &COLLECTIVE
     COLVAR 1
     INTERMOLECULAR T
    &END COLLECTIVE
  &END CONSTRAINT
&END MOTION
*******************************************************************


Two files used in this input are taken from the tests folder:

tests/Fist/sample_pot/water.pot has the following content:


*******************************************************************
BONDS
HT   HT      0.000     1.5139
OT   HT    450.000     0.9572

ANGLES
HT   OT   HT     55.000   104.5200

DIHEDRALS

IMPROPER

NONBONDED
HT     0.000000  -0.046000     0.224500
OT     0.000000  -0.152100     1.768200

HBOND CUTHB 0.5

END
*******************************************************************


tests/Fist/sample_pdb/water_2.pdb has the following content:

*******************************************************************
ATOM      1  OT  TIP3    1      -0.757  -5.616  -7.101  1.00
0.00      WAT  O
ATOM      2  HT  TIP3    1      -1.206  -5.714  -6.262  1.00
0.00      WAT  H
ATOM      3  HT  TIP3    1       0.024  -5.102  -6.896  1.00
0.00      WAT  H
ATOM      4  OT  TIP3    2     -11.317  -2.629  -9.689  1.00
0.00      WAT  O
ATOM      5  HT  TIP3    2     -11.021  -3.080 -10.480  1.00
0.00      WAT  H
ATOM      6  HT  TIP3    2     -10.511  -2.355  -9.252  1.00
0.00      WAT  H
*******************************************************************



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