Thermostats in QMMM with constraints

[shihao]

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
*******************************************************************