[CP2K-user] [CP2K:20447] Metadynamics 2 CVs
Leonardo Serafim
leoserafim89 at gmail.com
Fri Jul 12 19:09:15 UTC 2024
Dear CP2K Developers,
I hope this email finds you well. My name is Leonardo, and I am currently
working on simulations involving an endonuclease. I am reaching out to
request your assistance with my two collective variable (CV) metadynamics
simulation in CP2K.
In my study, I am using two CVs and 10 walkers. The path has already been
optimized using string method with the same CVs and 10 replicas. The CVs I
am using are:
1. The distance difference of the O-P bond (nucleophile-electrophile)
and the scissile P-O bond that dissociates.
2. The distance between the metal and the leaving group (Mg-O).
However, I am encountering an issue where the simulation stops when the
Gaussian is about to spawn. For instance, if I set NT_HILLS to 50, the
simulation stops at 50 steps. Interestingly, if I run the metadynamics
using only one of the CVs, it works perfectly.
I would appreciate any guidance or suggestions you can provide to resolve
this issue. I have attached my input file for your reference.
Thank you for your time and assistance.
Best regards,
----------
@SET PDB 1.pdb
@SET ID 1
@SET STEPS 10000
@SET WW 0.1
@SET HILLS 50
@SET TOP APE1.parm7
&GLOBAL
PROJECT APE1
PRINT_LEVEL LOW
RUN_TYPE MD
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
STRESS_TENSOR ANALYTICAL
&DFT
CHARGE -1
BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
POTENTIAL_FILE_NAME ./GTH_POTENTIALS
&MGRID
COMMENSURATE
CUTOFF 480
REL_CUTOFF 50
&END MGRID
&QS
METHOD GPW
EPS_DEFAULT 1.0E-8
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3
&END QS
&SCF
MAX_SCF 10
EPS_SCF 2.0E-6
SCF_GUESS HISTORY_RESTART
&OT
SAFE_DIIS T
STEPSIZE 0.15
ENERGY_GAP 0.1
MINIMIZER DIIS
PRECONDITIONER FULL_SINGLE_INVERSE
&END OT
&OUTER_SCF
EPS_SCF 2.0E-6
MAX_SCF 10
&END OUTER_SCF
&PRINT
&RESTART_HISTORY
ADD_LAST NUMERIC
BACKUP_COPIES 5 # ASPC order + 2
&EACH
__ROOT__ 1
MD 1
QS_SCF 0
&END EACH
&END RESTART_HISTORY
&END PRINT
&END SCF
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&XC_GRID
XC_DERIV SPLINE2_smooth
XC_SMOOTH_RHO NN10
&END XC_GRID
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME DFTD3
TYPE DFTD3
REFERENCE_FUNCTIONAL BLYP
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&END XC
&POISSON
POISSON_SOLVER WAVELET
PERIODIC NONE
&END POISSON
&END DFT
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME ${TOP}
&SPLINE
EMAX_SPLINE 1.0E8
RCUT_NB [angstrom] 10
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 96
O_SPLINE 6
&END EWALD
&END POISSON
&NEIGHBOR_LISTS
GEO_CHECK F
&END NEIGHBOR_LISTS
&END MM
&SUBSYS
&CELL
ABC [angstrom] 90 90 90
PERIODIC XYZ
&END CELL
&TOPOLOGY
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME ${TOP}
COORD_FILE_FORMAT PDB
COORD_FILE_NAME ${PDB}
&END TOPOLOGY
&KIND NA+
ELEMENT Na
&END KIND
&KIND CL-
ELEMENT Cl
&END KIND
&KIND H
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND P
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND MG
BASIS_SET TZV2P-GTH
POTENTIAL GTH-BLYP-q10
&END KIND
&COLVAR
&COMBINE_COLVAR
&COLVAR
&DISTANCE
ATOMS 5827 4693
&END DISTANCE
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 4693 4692
&END DISTANCE
&END COLVAR
FUNCTION CV1-CV2
VARIABLES CV1 CV2
ERROR_LIMIT 1.0E-8
&END COMBINE_COLVAR
&END COLVAR
&COLVAR
&DISTANCE
ATOMS 4692 5694
&END DISTANCE
&END COLVAR
&END SUBSYS
&QMMM
&CELL
ABC 20 20 20
PERIODIC XYZ
&END CELL
&WALLS
K 0.06
TYPE QUADRATIC
&END WALLS
E_COUPL GAUSS
CENTER SETUP_ONLY
NOCOMPATIBILITY T
USE_GEEP_LIB 10
&QM_KIND O
MM_INDEX 390 420 421 855 856 1988 2642 2643 2673 4696 4694 4695 4692
5827 5830 5833 4672 4702 4705
&END QM_KIND
&QM_KIND H
MM_INDEX 387 388 392 393 417 418 849 850 852 853 1980 1981 1984 1986
1989 1991 1993 2639 2640 2670 2671 2675 2676 4217 4218 4221 4223 4225 4227
4698 4688 4699 5828 5829 5831 5832 5834 5835 4690 4691 4671 4674 4701 4708
4711 4710 4704 4706
&END QM_KIND
&QM_KIND C
MM_INDEX 386 389 416 419 848 851 854 1979 1982 1983 1985 1987 1990
1992 2638 2641 2669 2672 4216 4219 4222 4226 4697 4687 4670 4673 4689 4700
4707 4709 4703
&END QM_KIND
&QM_KIND N
MM_INDEX 391 2674 4220 4224
&END QM_KIND
&QM_KIND P
MM_INDEX 4693
&END QM_KIND
&QM_KIND MG
MM_INDEX 5694
&END QM_KIND
&LINK
QM_INDEX 386
MM_INDEX 384
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 416
MM_INDEX 414
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 848
MM_INDEX 846
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 1979
MM_INDEX 1977
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 2638
MM_INDEX 2636
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 2669
MM_INDEX 2667
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 4216
MM_INDEX 4214
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 4707
MM_INDEX 4712
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 4673
MM_INDEX 4675
LINK_TYPE IMOMM
&END LINK
&LINK
QM_INDEX 4670
MM_INDEX 4667
LINK_TYPE IMOMM
&END LINK
&END QMMM
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
TIMESTEP [fs] 0.5
STEPS ${STEPS}
TEMPERATURE 300
&THERMOSTAT
TYPE NOSE
REGION GLOBAL
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 50
MTS 2
&END NOSE
&END THERMOSTAT
&END MD
&FREE_ENERGY
METHOD METADYN
&METADYN
DO_HILLS
NT_HILLS ${HILLS}
WW [kcalmol] ${WW}
&METAVAR
SCALE 0.1
COLVAR 1
&WALL
POSITION 2
TYPE QUADRATIC
&QUADRATIC
DIRECTION WALL_PLUS
K 0.01
&END QUADRATIC
&END WALL
&WALL
POSITION -2
TYPE QUADRATIC
&QUADRATIC
DIRECTION WALL_MINUS
K 0.01
&END QUADRATIC
&END WALL
&END METAVAR
&METAVAR
SCALE 0.1
COLVAR 2
&WALL
POSITION 4.5
TYPE QUADRATIC
&QUADRATIC
DIRECTION WALL_PLUS
K 0.01
&END QUADRATIC
&END WALL
&WALL
POSITION 2.0
TYPE QUADRATIC
&QUADRATIC
DIRECTION WALL_MINUS
K 0.01
&END QUADRATIC
&END WALL
&END METAVAR
&MULTIPLE_WALKERS
NUMBER_OF_WALKERS 10
WALKER_COMM_FREQUENCY 1
WALKER_ID ${ID}
&WALKERS_FILE_NAME
/home/leo/Documents/APE1/MTD/WALK1/walk1.dat
/home/leo/Documents/APE1/MTD/WALK2/walk2.dat
/home/leo/Documents/APE1/MTD/WALK3/walk3.dat
/home/leo/Documents/APE1/MTD/WALK4/walk4.dat
/home/leo/Documents/APE1/MTD/WALK5/walk5.dat
/home/leo/Documents/APE1/MTD/WALK6/walk6.dat
/home/leo/Documents/APE1/MTD/WALK7/walk7.dat
/home/leo/Documents/APE1/MTD/WALK8/walk8.dat
/home/leo/Documents/APE1/MTD/WALK9/walk9.dat
/home/leo/Documents/APE1/MTD/WALK10/walk10.dat
&END WALKERS_FILE_NAME
&END MULTIPLE_WALKERS
&PRINT
&COLVAR
COMMON_ITERATION_LEVELS 4
&EACH
MD 1
&END EACH
&END COLVAR
&END PRINT
&END METADYN
&END FREE_ENERGY
&PRINT
&TRAJECTORY
FORMAT DCD
&EACH
MD 4
&END EACH
&END TRAJECTORY
&RESTART_HISTORY
&EACH
MD 50
&END EACH
&END RESTART_HISTORY
&END PRINT
&END MOTION
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