[CP2K-user] [CP2K:19432] Re: Metadynamics CV adding bias for bond contraction?
Marcella Iannuzzi
marci.akira at gmail.com
Thu Oct 26 09:11:43 UTC 2023
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
On Tuesday, October 24, 2023 at 5:18:21 PM UTC+2 Liam H wrote:
> 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
>
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