Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part2_MM/plumed_PB4_MM.dat
Originally used with PLUMED version: 2.7
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

MOLINFO STRUCTURE=../template.pdb
WHOLEMOLECULES ENTITY0=1-166

s1: CENTER ATOMS=@back-1 NOPBC 
s2: CENTER ATOMS=@back-2 NOPBC
s3: CENTER ATOMS=@back-3 NOPBC
s4: CENTER ATOMS=@back-4 NOPBC
s5: CENTER ATOMS=@back-5 NOPBC
s6: CENTER ATOMS=@back-6 NOPBC
s7: CENTER ATOMS=@back-7 NOPBC
s8: CENTER ATOMS=@back-8 NOPBC
s9: CENTER ATOMS=@back-9 NOPBC
s10: CENTER ATOMS=@back-10 NOPBC

ALPHABETA ...
NOPBC
LABEL=back
REFERENCE=0
ATOMS1=@psi-1    COEFFICIENT1=-0.01427455
ATOMS2=@phi-2    COEFFICIENT2=-0.03003557
ATOMS3=@psi-2    COEFFICIENT3=-0.23777775
ATOMS4=@phi-3    COEFFICIENT4=0.139227
ATOMS5=@psi-3    COEFFICIENT5=0.26525215
ATOMS6=@phi-4    COEFFICIENT6=-0.18108167
ATOMS7=@psi-4    COEFFICIENT7=0.01530576
ATOMS8=@phi-5    COEFFICIENT8=0.07231603
ATOMS9=@psi-5    COEFFICIENT9=-0.1183752
ATOMS10=@phi-6  COEFFICIENT10=0.00089293
ATOMS11=@psi-6  COEFFICIENT11=-0.23744683
ATOMS12=@phi-7  COEFFICIENT12=0.15661255
ATOMS13=@psi-7  COEFFICIENT13=0.63855605
ATOMS14=@phi-8  COEFFICIENT14=-0.15161411
ATOMS15=@psi-8  COEFFICIENT15=0.50759965
ATOMS16=@phi-9  COEFFICIENT16=-0.04886669
ATOMS17=@psi-9  COEFFICIENT17=0.13599118
ATOMS18=@phi-10 COEFFICIENT18=-0.1007816
...
          
cmap: CONTACTMAP ...
NOPBC
SWITCH={RATIONAL R_0=0.6}
ATOMS1=s1,s4     WEIGHT1=0.02521988
ATOMS2=s1,s5     WEIGHT2=0.20455216
ATOMS3=s1,s6     WEIGHT3=-0.54414755
ATOMS4=s1,s7     WEIGHT4=0.36219968
ATOMS5=s1,s8     WEIGHT5=0.1279484
ATOMS6=s1,s9     WEIGHT6=-0.22453008
ATOMS7=s1,s10    WEIGHT7=0.29550159
ATOMS8=s2,s5     WEIGHT8=-0.03385588
ATOMS9=s2,s6     WEIGHT9=0.09919236
ATOMS10=s2,s7   WEIGHT10=-0.03330457
ATOMS11=s2,s8   WEIGHT11=-0.13847136
ATOMS12=s2,s9   WEIGHT12=0.39094173
ATOMS13=s2,s10  WEIGHT13=-0.1983029
ATOMS14=s3,s6   WEIGHT14=-0.02328201
ATOMS15=s3,s7   WEIGHT15=0.0069981
ATOMS16=s3,s8   WEIGHT16=0.2231250
ATOMS17=s3,s9   WEIGHT17=-0.25618473
ATOMS18=s3,s10  WEIGHT18=0.113674
ATOMS19=s4,s7   WEIGHT19=0.01257499
ATOMS20=s4,s8   WEIGHT20=-0.01498744
ATOMS21=s4,s9   WEIGHT21=-0.11663488
ATOMS22=s4,s10  WEIGHT22=0.084924
ATOMS23=s5,s8   WEIGHT23=-0.005496
ATOMS24=s5,s9   WEIGHT24=0.03150733
ATOMS25=s5,s10  WEIGHT25=-0.03456732
ATOMS26=s6,s9   WEIGHT26=0.00233215
ATOMS27=s6,s10  WEIGHT27=0.01574143
ATOMS28=s7,s10  WEIGHT28=-0.01026257
SUM
...

rg: GYRATION ATOMS=@N-1,@CA-1,@C-1,@N-2,@CA-2,@C-2,@N-3,@CA-3,@C-3,@N-4,@CA-4,@C-4,@N-5,@CA-5,@C-5,@N-6,@CA-6,@C-6,@N-7,@CA-7,@C-7,@N-8,@CA-8,@C-8,@N-9,@CA-9,@C-9,@N-10,@CA-10,@C-10 NOPBC
hh: ANTIBETARMSD RESIDUES=all TYPE=DRMSD R_0=0.1 STRANDS_CUTOFF=1 NOPBC

mm: PBMETAD ... 
ARG=back,cmap,rg,hh 
SIGMA_MAX=0.2,0.2,0.2,0.2 
SIGMA_MIN=0.01,0.001,0.004,0.02 
SIGMA=0.015 ADAPTIVE=GEOM 
GRID_MIN=-4,-2,0.3,0 
GRID_MAX=4,2,1.4,3
HEIGHT=0.5 BIASFACTOR=10 PACE=200 
WALKERS_MPI 
FILE=../HILLS.back,../HILLS.cmap,../HILLS.rg,../HILLS.hh
GRID_WFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh
#GRID_RFILES=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh
GRID_WSTRIDE=10000000
...

SAXS ...
        NOPBC
        #GPU
        LABEL=saxs
        ATOMS=1-166  
        ATOMISTIC
        SCALEINT=100

	QVALUE1=0.010000	EXPINT1=99.884787
	QVALUE2=0.070000	EXPINT2=94.573283
	QVALUE3=0.130000	EXPINT3=82.964898
	QVALUE4=0.190000	EXPINT4=68.296624
	QVALUE5=0.250000	EXPINT5=53.565198
	QVALUE6=0.310000	EXPINT6=40.540191
	QVALUE7=0.370000	EXPINT7=29.869842
	QVALUE8=0.430000	EXPINT8=21.605034
	QVALUE9=0.490000	EXPINT9=15.542217
	QVALUE10=0.550000	EXPINT10=11.346918
	QVALUE11=0.610000	EXPINT11=8.628281
	QVALUE12=0.670000	EXPINT12=7.008095
	QVALUE13=0.730000	EXPINT13=6.154012
	QVALUE14=0.790000	EXPINT14=5.789840
	QVALUE15=0.850000	EXPINT15=5.711048
	QVALUE16=0.910000	EXPINT16=5.799616
	QVALUE17=0.970000	EXPINT17=6.016059
	QVALUE18=1.030000	EXPINT18=6.361548
	QVALUE19=1.090000	EXPINT19=6.825863
	QVALUE20=1.150000	EXPINT20=7.352355	
	QVALUE21=1.210000	EXPINT21=7.844432
	QVALUE22=1.270000	EXPINT22=8.208167
	QVALUE23=1.330000	EXPINT23=8.399227
	QVALUE24=1.390000	EXPINT24=8.442345

        DOSCORE
        REWEIGHT ARG=mm.bias
        NOISETYPE=MGAUSS
        SCALEDATA  SCALE_PRIOR=FLAT SCALE0=1.00 SCALE_MIN=0.5 SCALE_MAX=1.5 DSCALE=0.0002
        SIGMA0=1
        SIGMA_MIN=0.001
        MC_CHUNKSIZE=2 MC_STEPS=12 
        SIGMA_MEAN0=3
        OPTSIGMAMEAN=SEM_MAX 
	AVERAGING=200
        WRITE_STRIDE=10000
... SAXS

BIASVALUE ARG=saxs.score STRIDE=2

ens: ENSEMBLE ARG=(saxs\.q-.*),mm.bias REWEIGHT
st: STATS ARG=(ens\.saxs\.q-.*) PARARG=(saxs\.exp-.*)

PRINT ARG=(saxs\.score),(saxs\.biasDer),(saxs\.weight),(saxs\.neff),(saxs\.scale),(saxs\.acceptScale),(saxs\.acceptSigma),(saxs\.sigma.*)  FILE=BAYES STRIDE=5000
PRINT ARG=st.*,(ens\.saxs\.q-.*) FILE=STATS STRIDE=5000
#PRINT ARG=(saxs\.q-.*)  FILE=QVALUE STRIDE=5000

PRINT ARG=back,cmap,rg,hh FILE=COLVAR STRIDE=5000