Restart MD

Sandeep Kumar Reddy kuma... at gmail.com
Wed Nov 23 07:28:54 CET 2011


Dear all,
            I am doing an MD run by restraining dihedral to some value.  I
have a problem with restarting this job.  When i used the following options
to restart this, the value of COLVAR 1  before and after restart are not
same.

Input file :

&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT
    POTENTIAL_FILE_NAME POTENTIAL
    CHARGE = 0
    &MGRID
      CUTOFF 280
      NGRIDS 5
      REL_CUTOFF 40
    &END MGRID
     &QS
       METHOD GPW
       EPS_DEFAULT 1.0E-10
     &END QS
     &SCF
       SCF_GUESS RESTART
       EPS_SCF 1.0E-6
       MAX_SCF 150
#       MIXING 0.3
       &OUTER_SCF
          EPS_SCF 1.0E-6
          MAX_SCF 50
       &END
    &OT
          MINIMIZER CG
          PRECONDITIONER FULL_ALL
          ENERGY_GAP 0.001
          STEPSIZE 0.05
       &END

    &END SCF
    &XC
     &XC_FUNCTIONAL BLYP
      &END XC_FUNCTIONAL
      &XC_GRID
        XC_SMOOTH_RHO NN50
        XC_DERIV SPLINE2
      &END
      &vdW_POTENTIAL
         DISPERSION_FUNCTIONAL PAIR_POTENTIAL
         &PAIR_POTENTIAL
            TYPE DFTD2
            REFERENCE_FUNCTIONAL BLYP
         &END PAIR_POTENTIAL
      &END vdW_POTENTIAL

   &END XC
  &END DFT

  &SUBSYS
    &CELL
      ABC 12.16174 12.16174 12.16174
    &END CELL

    &COORD
     @INCLUDE coor.xyz
    &END COORD

     &KIND O
      BASIS_SET TZV2P-MOLOPT-GTH-q6
      POTENTIAL GTH-BLYP-q6
    &END KIND

    &KIND C
      BASIS_SET TZV2P-MOLOPT-GTH-q4
      POTENTIAL GTH-BLYP-q4
    &END KIND

    &KIND H
      BASIS_SET TZV2P-MOLOPT-GTH-q1
      POTENTIAL GTH-BLYP-q1
#      MASS 2.016
    &END KIND

    &COLVAR
      &TORSION
        ATOMS  179 178 181 180
      &END
    &END
    &COLVAR
      &DISTANCE
        ATOMS  180 181
      &END
    &END
    &COLVAR
      &TORSION
         ATOMS  179 178 182 183
      &END
    &END
    &COLVAR
      &DISTANCE
        ATOMS  182 183
      &END
    &END


  &END SUBSYS
&END FORCE_EVAL

&GLOBAL
  PROJECT OUT-CA-AA-MD
  RUN_TYPE MD
  PRINT_LEVEL MEDIUM
&END GLOBAL

&MOTION
  &MD
    ENSEMBLE NVT
    STEPS 10000
    TIMESTEP 0.5
    &THERMOSTAT
      &NOSE
        LENGTH 3
        YOSHIDA 3
        TIMECON 100.0
        MTS 2
      &END NOSE
    &END THERMOSTAT
  TEMPERATURE 300.0
  &END MD

  &FREE_ENERGY
    &METADYN
      DO_HILLS .FALSE.
      &METAVAR
        COLVAR 1
        SCALE 1.
      &END
      &PRINT
        &COLVAR
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
      &END
      &METAVAR
        COLVAR 2
        SCALE 1.
      &END
      &PRINT
        &COLVAR
          COMMON_ITERATION_LEVELS 3
          &EACH
             MD 1
          &END
        &END
      &END
      &METAVAR
        COLVAR 2
        SCALE 1.
      &END
      &PRINT
        &COLVAR
          COMMON_ITERATION_LEVELS 3
          &EACH
             MD 1
          &END
        &END
      &END
      &METAVAR
        COLVAR 3
        SCALE 1.
      &END
      &PRINT
        &COLVAR
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
      &END
    &END
  &END

  &CONSTRAINT
    &CONSTRAINT_INFO
      &EACH
        MD 1
      &END
    &END
    &COLLECTIVE
      COLVAR 1
      INTERMOLECULAR 1
      TARGET 0.00
      TARGET_GROWTH  0.001
      TARGET_LIMIT   0.872647
      &RESTRAINT
        K [kcalmol]  20.0000
      &END
    &END
  &END
  &PRINT
    &VELOCITIES
      &EACH
        MD 1
      &END
    &END
    &FORCES
      &EACH
        MD 1
      &END
    &END
  &END

&END MOTION

&EXT_RESTART
    RESTART_FILE_NAME OUT-CA-AA-MD-1.restart
    RESTART_COUNTERS  T
    RESTART_POS  T
    RESTART_VEL  T
    RESTART_CONSTRAINT T
    RESTART_METADYNAMICS F
&END EXT_RESTART


--------------

Before restart, the  COLVAR file contains ..


  1470.0      0.70287      2.00213      2.00213     -0.23927
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1470.5      0.70864      1.98593      1.98593     -0.23249
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1471.0      0.71401      1.96755      1.96755     -0.22558
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1471.5      0.71885      1.94803      1.94803     -0.21857
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1472.0      0.72302      1.92860      1.92860     -0.21149
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1472.5      0.72638      1.91055      1.91055     -0.20437
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1473.0      0.72881      1.89520      1.89520     -0.19724
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1473.5      0.73017      1.88373      1.88373     -0.19014
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1474.0      0.73037      1.87703      1.87703     -0.18308
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000


After restart,


      1470.5      0.70596      1.98584      1.98584     -0.23193
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1471.0      0.70867      1.96732      1.96732     -0.22446
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000
      1471.5      0.71088      1.94763      1.94763     -0.21691
0.00000      0.00000      0.00000      0.00000      0.00000
0.00000      0.00000      0.00000      0.00000      0.00000


As can be seen, COLVAR1  value is not same at 1470.5, 1471.0 so on .. th
time step.   And also, ener file output is

Before restart,

     2941         1470.500000         0.264232649       305.633596492
-1071.124343277     -1070.837205951       110.006900000
      2942         1471.000000         0.262352431       303.458778818
-1071.122443287     -1070.837141220       126.382300000
      2943         1471.500000         0.258554740       299.066050830
-1071.118558109     -1070.837008858       109.594400000
      2944         1472.000000         0.254843481       294.773298732
-1071.114769705     -1070.836887261       108.996200000
      2945         1472.500000         0.253037023       292.683797430
-1071.112972727     -1070.836852718       109.157400000
      2946         1473.000000         0.253686059       293.434527505
-1071.113732934     -1070.836919998       125.062900000
      2947         1473.500000         0.255812040       295.893615199
-1071.116023855     -1070.837040816       108.843300000
      2948         1474.000000         0.257604549       297.966981110
-1071.117955614     -1070.837135519       125.324700000


after restart,


      2941         1470.500000         0.264119595       305.502828525
-1071.124357212     -1070.837332951       540.249300000
      2942         1471.000000         0.262260456       303.352392372
-1071.122478947     -1070.837268889       203.759400000
      2943         1471.500000         0.258489935       298.991092511
-1071.118620866     -1070.837136476       203.167400000
      2944         1472.000000         0.254807453       294.731625484
-1071.114861358     -1070.837015022       178.069300000



Can anybody help me out how to restart the job?

Thanks.

Regards,
Sandeep
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