Metadynamics CV adding bias for bond contraction?

[Liam H]

Hello,

So I have a kind of general question, normally when I run metadynamics simulations, unimolecular the systems where a bond needs to be broken works easily with the bond distance CV.

But in the reverse case, a bimolecular system where bias needs to be added to make a bond form, or even a unimolecular system with flexible chains that need to cyclize, these systems tend to get get further and further apart instead of closer together..

Does anyone have any tips on how to remedy this? This is an example of my input parameters (minus DFT and print sections), This is a unimolecular acyclic system that I am attempting to show cyclization in metadynamics. I ran only 10 000 steps so I could do more but it did not seem to make any progress.. the CVs don't really change at all

Thank you,
Liam

&GLOBAL
  PROJECT TS-1
  PRINT_LEVEL LOW
  RUN_TYPE MD
&END GLOBAL

&FORCE_EVAL
  METHOD Quickstep
  &SUBSYS
    &CELL
      A    16.30464600     0.00000000     0.00000000
      B     0.00000000    16.90186000     0.00000000
      C     0.00000000     0.00000000    17.81548400
      PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)
    &END CELL
    &COORD
      C           1.05566000    0.66730000   -0.06403000
      C           1.16646000   -0.73817000   -0.01172000
      C           2.41800000   -1.28561000    0.31373000
      C           3.52794000   -0.48197000    0.56970000
      C           3.41209000    0.90158000    0.47292000
      C           2.18170000    1.46806000    0.15045000
      C          -0.23374000    1.36196000   -0.37069000
      C          -0.39935000    1.82258000   -1.68125000
      C          -1.55390000    2.49392000   -2.07260000
      C          -2.57130000    2.71290000   -1.14716000
      C          -2.42186000    2.25411000    0.15599000
      C          -1.25880000    1.58006000    0.58740000
      B          -1.19524000    1.14740000    2.08650000
      Br          0.40816000    0.79973000    3.07109000
      Br         -2.82356000    0.97103000    3.10636000
      Si         -0.22795000   -1.94672000   -0.40552000
      C           0.41691000   -3.70245000   -0.32700000
      C          -1.77233000   -1.79184000    0.63917000
      Br         -0.85948000   -1.61419000   -2.55308000
      H           2.53894000   -2.36934000    0.36673000
      H           4.48380000   -0.93949000    0.82873000
      H           4.27648000    1.54227000    0.65408000
      H           2.07625000    2.55335000    0.09152000
      H           0.39256000    1.62706000   -2.40625000
      H          -1.65976000    2.83803000   -3.10259000
      H          -3.48256000    3.23620000   -1.43897000
      H          -3.22803000    2.42901000    0.86879000
      H          -0.38316000   -4.39064000   -0.63509000
      H           1.27092000   -3.84940000   -1.00275000
      H           0.72280000   -3.96581000    0.69732000
      H          -2.41046000   -2.66949000    0.45752000
      H          -2.35096000   -0.89299000    0.39003000
      H          -1.51622000   -1.76845000    1.71066000
    &END COORD

    &COLVAR
       &DISTANCE
          ATOMS 2 13
       &END DISTANCE
&END COLVAR

    &COLVAR
       &DISTANCE
          ATOMS 2 16
       &END DISTANCE
&END COLVAR



#   &VELOCITY #inital velocity
#   &END VELOCITY
    &KIND C      
      ELEMENT C
      BASIS_SET DZVP-MOLOPT-SR-GTH-q4
      POTENTIAL GTH-PBE
    &END KIND
    &KIND Si      
      ELEMENT Si
      BASIS_SET DZVP-MOLOPT-SR-GTH-q4
      POTENTIAL GTH-PBE
    &END KIND
    &KIND Br      
      ELEMENT Br
      BASIS_SET DZVP-MOLOPT-SR-GTH-q7
      POTENTIAL GTH-PBE
    &END KIND
    &KIND B      
      ELEMENT B
      BASIS_SET DZVP-MOLOPT-SR-GTH-q3
      POTENTIAL GTH-PBE
    &END KIND
    &KIND H      
      ELEMENT H
      BASIS_SET DZVP-MOLOPT-SR-GTH-q1
      POTENTIAL GTH-PBE
    &END KIND
  &END SUBSYS

&MOTION
  &MD
    ENSEMBLE NVE
    STEPS 10000 #Number of steps to run
    TIMESTEP 0.5 #Step size in fs
    TEMPERATURE 400.0 #Initial and maintained temperature (K)
    ANGVEL_ZERO T #Eliminate overall rotation component from initial velocity
    &PRINT
      &PROGRAM_RUN_INFO
        &EACH
          MD     1 #Output frequency of MD information, 0 means never
        &END EACH
      &END PROGRAM_RUN_INFO
    &END PRINT
  &END MD
  &FREE_ENERGY
    &METADYN
      DO_HILLS
      NT_HILLS 50
      WW 3.0e-3
      TEMPERATURE 400
      TEMP_TOL  10.0
      WELL_TEMPERED
      DELTA_T 6000
      COLVAR_AVG_TEMPERATURE_RESTART 400

      &METAVAR
        SCALE 0.2
        COLVAR 1
      &END METAVAR

      &METAVAR
        SCALE 0.2
        COLVAR 2
      &END METAVAR

      &PRINT
        &COLVAR
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
        &HILLS
           COMMON_ITERATION_LEVELS 3
           &EACH
             MD 1
           &END
        &END
      &END
    &END METADYN
  &END

  &PRINT
    &TRAJECTORY
      &EACH
        MD   1 #Output frequency of coordinates, 0 means never
      &END EACH
      FORMAT xyz
    &END TRAJECTORY
    &VELOCITIES
      &EACH
        MD     0 #Output frequency of velocities, 0 means never
      &END EACH
    &END VELOCITIES
    &FORCES
      &EACH
        MD     0 #Output frequency of forces, 0 means never
      &END EACH
    &END FORCES
    &RESTART
      BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never
      &EACH
        MD  1 #Frequency of updating last restart file, 0 means never
      &END EACH
    &END RESTART
    &RESTART_HISTORY OFF
    &END RESTART_HISTORY
  &END PRINT
&END MOTION

[Marcella Iannuzzi]

Dear Liam

Metadynamics operates to alter the value of CV along the path of least energy.

The FES appears smoother and less steep when the molecules move apart instead of toward each other,  which is logical. 

Distances display quite a large range of variability and it may take a long time to explore the space defined by distances, even though the configurations at different distances relate to the same "chemical state", i.e., separated molecules. 

Other variables, as coordination, may prove more effective, as the "separated molecules" state corresponds to a coordination of zero. After exploring this region of the space, it is expected that the algorithm will search for other regions of coordination greater than zero. 

An alternative, approach would be to narrow the range of variability in distances by applying a restraining potential. 

Regards

Marcella

[Liam H]

Hi Marcella,

Thank you, this is very helpful, makes a lot of sense. I will give both these options a try to see if I can make it work for my system as well as run my simulations longer.

Best,
Liam

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