[CP2K-user] [CP2K:20449] Re: Metadynamics 2 CVs
Marcella Iannuzzi
marci.akira at gmail.com
Sun Jul 14 10:41:49 UTC 2024
Hi Leonardo
The input seems OK
Have you got any error message?
Does it work with anyone of the CVs if alone?
Have you tried with a simplified input, for instance without walls, without
multiple walkers?
Does it work without crashing if you set DO_HILLS to false?
Regards
Marcella
On Friday, July 12, 2024 at 9:56:20 PM UTC+2 leoser... at gmail.com wrote:
> 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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