Project ID: plumID:20.007
Source: single/plumed.dat
Originally used with PLUMED version: 2.4.2
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# The commented out lines are the original implementation. They have been altered to be compatible with newer PLUMED versions.

RESTART

MOLINFO STRUCTURE=reference.pdb MOLTYPE=protein
WHOLEMOLECULES ENTITY0=1-2604  
rmsd: RMSD REFERENCE=rmsd.pdb TYPE=OPTIMAL

d-r28_l110: DISTANCE ATOMS=@CA-28,@CA-110
d-l110_l118: DISTANCE ATOMS=@CA-110,@CA-118
d-r85_l112: DISTANCE ATOMS=@CA-85,@CA-112
d-r157_l116: DISTANCE ATOMS=@CA-157,@CA-116
d-r25_l115: DISTANCE ATOMS=@CA-25,@CA-115
d-l111_l112: DISTANCE ATOMS=@CA-111,@CA-112
d-r97_l115: DISTANCE ATOMS=@CA-97,@CA-115
d-r142_l119: DISTANCE ATOMS=@CA-142,@CA-119
d-r154_l113: DISTANCE ATOMS=@CA-154,@CA-113
d-r67_l116: DISTANCE ATOMS=@CA-67,@CA-116
d-r43_l114: DISTANCE ATOMS=@CA-43,@CA-114
d-r34_l114: DISTANCE ATOMS=@CA-34,@CA-114
d-r34_l118: DISTANCE ATOMS=@CA-34,@CA-118
d-l112_l113: DISTANCE ATOMS=@CA-112,@CA-113
d-r49_l116: DISTANCE ATOMS=@CA-49,@CA-116
d-l115_l116: DISTANCE ATOMS=@CA-115,@CA-116

d1769_1819: DISTANCE ATOMS=1769,1819
psi_114_1: TORSION ATOMS=1770,1772,1788,1790


COMBINE ...
LABEL=rc1 ARG=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116
COEFFICIENTS=5.690912902355194092e-02,-1.696033775806427002e-01,-1.088943518698215485e-02,-3.811309486627578735e-02,-3.845035657286643982e-02,-3.398763835430145264e-01,6.818664073944091797e-01,1.402324438095092773e-01,5.613043904304504395e-02,1.617383360862731934e-01,8.190712332725524902e-02,-2.790833413600921631e-01,4.563379585742950439e-01,1.509449779987335205e-01,4.242382943630218506e-02,-1.344945281744003296e-01 PERIODIC=NO
... COMBINE



COMBINE ...
LABEL=rc2 ARG=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116
COEFFICIENTS=-1.883340626955032349e-01,4.097261726856231689e-01,1.357467919588088989e-01,4.463798403739929199e-01,-1.859887838363647461e-01,2.378992550075054169e-02,-3.209500312805175781e-01,4.577260613441467285e-01,1.797014027833938599e-01,3.510920107364654541e-01,-1.946701705455780029e-01,-2.567137824371457100e-03,1.762732118368148804e-01,-7.985947653651237488e-03,-7.434802502393722534e-02,-3.417430073022842407e-02 PERIODIC=NO
... COMBINE


METAD ...
LABEL=metad
ARG=rc1,rc2
PACE=500
HEIGHT=1.5
SIGMA=0.05,0.05
BIASFACTOR=10.0
#GRID_MIN=1.00,0.21
#GRID_MAX=5.50,4.70
#GRID_BIN=300,300
#REWEIGHTING_NGRID=300,300
TEMP=300.0
... METAD


UPPER_WALLS ARG=rmsd AT=0.5 KAPPA=1000.0 EXP=4 EPS=1 OFFSET=0 LABEL=uwall


#PRINT ARG=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116,rc1,rc2,uwall.bias,metad.bias,metad.rbias STRIDE=1 FILE=COLVAR
#PRINT ARG=d1769_1819,psi_114_1,rmsd,uwall.bias,metad.bias,metad.rbias STRIDE=50 FILE=COLVAR_strucutre

PRINT ARG=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116,rc1,rc2,uwall.bias,metad.bias STRIDE=1 FILE=COLVAR
PRINT ARG=d1769_1819,psi_114_1,rmsd,uwall.bias,metad.bias STRIDE=50 FILE=COLVAR_strucutre