[CP2K-user] [CP2K:19419] Metadynamics CV adding bias for bond contraction?
Liam H
nmrmoose at gmail.com
Tue Oct 24 15:18:21 UTC 2023
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
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/7672b266-e542-4864-8013-fcda826fbefan%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20231024/b26203f6/attachment-0001.htm>
More information about the CP2K-user
mailing list