[CP2K-user] umbrella sampling

Wei Zhang zwei88... at gmail.com
Fri Dec 21 10:15:20 UTC 2018


Dear Sandeep,
I was also doing some work with Umbrella sampling, and with help of Pietro, 
I got the file of **.metadynLog. However, I am not sure what is the meaning 
and unit of the data, and how could it be used to calculate the energy?
Your kindness help will be appreciated.

Wei Zhang

在 2011年11月19日星期六 UTC+8上午2:02:31,sandeep写道:
>
> Thanks  alot.
>
> On Nov 18, 1:54 pm, Pietro Vidossich <v.... at klingon.uab.es> wrote:
> > Hello,
> >
> > �I used the PRINT directive of the FREE_ENERGY module, as shown below. 
> regards, pietro
> >
> > �&FREE_ENERGY
> > �� &METADYN
> > ���� DO_HILLS .FALSE.
> > ���� &METAVAR
> > ������ COLVAR 1
> > ������ SCALE 1.
> > ���� &END
> > ���� &PRINT
> > ������ &COLVAR
> > ��������� COMMON_ITERATION_LEVELS 3
> > �������� &EACH
> > ���������� MD 1
> > �������� &END
> > ������ &END
> > ���� &END
> > �� &END METADYN
> > �&END FREE_ENERGY
> >
> > On Fri, 18 Nov 2011 10:36:08 +0530, Sandeep Kumar Reddy wrote
> >
> >
> >
> >
> >
> >
> >
> > > Dear all,
> > > ������������ I would like to do umbrella 
> sampling using cp2k. For this, i have defined a collective variable and� 
> i used restraint option to put an umbrella at CV value.
> > > I wanted cp2k to print the value of collective variable at each MD 
> step. Can anybody help me which option does this job ?
> >
> > > Input file :
> >
> > > &FORCE_EVAL
> > > � METHOD Quickstep
> > > � &DFT
> > > ��� BASIS_SET_FILE_NAME BASIS_MOLOPT
> > > ��� POTENTIAL_FILE_NAME POTENTIAL
> > > ��� CHARGE = 0�
> > > ��� &MGRID
> > > ����� CUTOFF 200
> > > ����� NGRIDS 5
> > > ����� REL_CUTOFF 40
> > > ��� &END MGRID
> > > ���� &QS
> > > ������ METHOD GPW
> > > ������ EPS_DEFAULT 1.0E-10
> > > ���� &END QS
> > > ���� &SCF
> > > ������ SCF_GUESS ATOMIC
> > > ������ EPS_SCF 1.0E-5
> > > ������ MAX_SCF 1000
> > > #������ MIXING 0.3
> > > ������ &OUTER_SCF
> > > ��������� EPS_SCF 1.0E-3
> > > ��������� MAX_SCF 50
> > > ������ &END
> > > ��� &OT
> > > ��������� MINIMIZER CG
> > > ��������� PRECONDITIONER FULL_ALL
> > > ��������� ENERGY_GAP 0.001
> > > ��������� STEPSIZE 0.05
> > > ������ &END
> > > �
> > > ��� &END SCF
> > > ��� &XC
> > > ���� &XC_FUNCTIONAL BLYP
> > > ����� &END XC_FUNCTIONAL
> > > ����� &vdW_POTENTIAL
> > > �������� DISPERSION_FUNCTIONAL PAIR_POTENTIAL
> > > �������� &PAIR_POTENTIAL
> > > ����������� TYPE DFTD2
> > > ����������� REFERENCE_FUNCTIONAL BLYP
> > > �������� &END PAIR_POTENTIAL
> > > ����� &END vdW_POTENTIAL
> > > ������ &XC_GRID
> > > ������� XC_SMOOTH_RHO NN50
> > > ������� XC_DERIV SPLINE2
> > > ����� &END
> > > �� &END XC
> > > � &END DFT
> >
> > > � &SUBSYS
> > > ��� &CELL
> > > ����� ABC 10.0� 10.0 10.0
> > > ����� PERIODIC NONE
> > > ��� &END CELL
> >
> > > ��� &COORD
> > > ���� @INCLUDE coor.xyz
> > > ��� &END COORD
> >
> > > ���� &KIND O
> > > ����� BASIS_SET TZV2P-MOLOPT-GTH-q6
> > > ����� POTENTIAL GTH-BLYP-q6
> > > ��� &END KIND
> > > ���
> > > ��� &KIND C
> > > ����� BASIS_SET TZV2P-MOLOPT-GTH-q4
> > > ����� POTENTIAL GTH-BLYP-q4
> > > ��� &END KIND
> >
> > > ��� &KIND H
> > > ����� BASIS_SET TZV2P-MOLOPT-GTH-q1
> > > ����� POTENTIAL GTH-BLYP-q1
> > > ����� MASS 2.016
> > > ��� &END KIND
> >
> > > ��� &COLVAR
> > > ����� &TORSION
> > > ������� ATOMS 2� 1� 4� 3�
> > > ����� &END
> > > ����� &PRINT
> > > ������� &PROGRAM_RUN_INFO ON
> > > ��������� &EACH
> > > ����������� MD� 1
> > > ��������� &END
> > > ������� &END PROGRAM_RUN_INFO
> > > ����� &END PRINT
> > > ��� &END
> >
> > > � &END SUBSYS
> > > &END FORCE_EVAL
> >
> > > &GLOBAL
> > > � PROJECT OUT-CA-AS
> > > � RUN_TYPE MD
> > > � PRINT_LEVEL MEDIUM
> > > &END GLOBAL
> >
> > > &MOTION
> > > � &CONSTRAINT
> > > ��� &CONSTRAINT_INFO
> > > ����� &EACH
> > > ������� MD 1
> > > ����� &END
> > > ��� &END
> > > ��� &COLLECTIVE
> > > ����� COLVAR 1�
> > > ����� MOLECULE 1�
> > > ����� TARGET 0.0
> > > ����� TARGET_GROWTH� 0.001
> > > ����� TARGET_LIMIT 1.57
> > > ����� &RESTRAINT
> > > ������� K� 10.0�
> > > ����� &END
> > > ��� &END
> > > � &END
> > > � &PRINT
> > > ��� &VELOCITIES
> > > ����� &EACH
> > > ������� MD 1
> > > ����� &END
> > > ��� &END
> > > ��� &FORCES
> > > ����� &EACH
> > > ������� MD 1
> > > ����� &END
> > > ��� &END
> > > � &END
> > > � &MD
> > > ��� ENSEMBLE NVT
> > > ��� STEPS 4000
> > > ��� TIMESTEP 0.5
> > > ��� TEMPERATURE 298.15
> > > ��� &THERMOSTAT
> > > ����� TYPE CSVR
> > > ����� &CSVR
> > > ������� TIMECON [fs] 20.
> > > ����� &END
> > > ��� &END THERMOSTAT
> > > � &END MD
> > > &END MOTION
> >
> > > Regards,
> > > Sandeep
> >
> > > --
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>
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