[CP2K-user] [CP2K:20452] Re: Metadynamics 2 CVs
Marcella Iannuzzi
marci.akira at gmail.com
Tue Jul 16 08:05:23 UTC 2024
Hi Leo,
>From what you write I would guess that the problem is in the value of one
of the CV for one of the walkers and not in the definition of the CVs
themself.
On the other hand, tis would not explain why the simulation stops in the
middle of the SCF.
Do you observe anything wrong in the values of the CVs for any of the 10
walkers?
Is there a particular walker that triggers the crash, or is just the number
of walkers?
If you say that the simulation runs with one CV, I doubt that this is a
hardware problem.
Adding one CV does not affect the resources needs.
DO_HILLS F sets a run where no hills are spawned.
Regards
Marcella
On Monday, July 15, 2024 at 11:03:45 PM UTC+2 leoser... at gmail.com wrote:
> Hello Marcella,
>
> Thank you for your reply.
>
> Unfortunately I do not get any error message, I checked the output file
> for every walker. The simulation stops in the middle of a SCF.
>
> I am able to run the MTD using only one CV, and the energy barrier is very
> close to the experimental value. However, to address the role of the metal,
> which is an important point in our paper, we would like to perform a MTD
> simulation with 2 CVs.
>
> I followed your suggestions and I was able to run the simulation with 5
> walkers, no walls and with DO_HILLS .false.. However, I was not able to
> perform the same simulation with 10 walkers.
>
> Do you think that might be a hardware issue? My workstation has two CPUs
> (AMD EPYC 7713 64-Core) and 264 GB ram.
>
> Also, would you please explain what is the difference of using DO_HILLS
> T/F?
>
> Best,
>
> Leo
>
>
>
>
>
>
>
> On Sunday, July 14, 2024 at 6:41:49 AM UTC-4 Marcella Iannuzzi wrote:
>
>> 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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