[CP2K-user] [CP2K:19436] Re: Metadynamics CV adding bias for bond contraction?
Liam H
nmrmoose at gmail.com
Thu Oct 26 20:58:58 UTC 2023
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
On Thu, Oct 26, 2023 at 6:41 AM Marcella Iannuzzi <marci.akira at gmail.com>
wrote:
>
>
> 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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