PLUMED-NEST

Project ID: plumID:21.019
Source: Ibuprofen_Overprediction/plumed_RDF.dat
Originally used with PLUMED version: 2.5-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# Define Centers of atoms (Mass-Charge file required)
RDF_c1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1,2,4,6,7,8,10,11,13,16,18,20,22,26,30
RDF_c2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=34,35,37,39,40,41,43,44,46,49,51,53,55,59,63
RDF_c3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=67,68,70,72,73,74,76,77,79,82,84,86,88,92,96
RDF_c4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=100,101,103,105,106,107,109,110,112,115,117,119,121,125,129
...
RDF_c284 COM 
ATOMS
the list of atoms which are involved the virtual atom's definition
=9340,9341,9343,9345,9346,9347,9349,9350,9352,9355,9357,9359,9361,9365,9369
RDF_c285 COM 
ATOMS
the list of atoms which are involved the virtual atom's definition
=9373,9374,9376,9378,9379,9380,9382,9383,9385,9388,9390,9392,9394,9398,9402
RDF_c286 COM 
ATOMS
the list of atoms which are involved the virtual atom's definition
=9406,9407,9409,9411,9412,9413,9415,9416,9418,9421,9423,9425,9427,9431,9435
RDF_c287 COM 
ATOMS
the list of atoms which are involved the virtual atom's definition
=9439,9440,9442,9444,9445,9446,9448,9449,9451,9454,9456,9458,9460,9464,9468
RDF_c288 COM 
ATOMS
the list of atoms which are involved the virtual atom's definition
=9472,9473,9475,9477,9478,9479,9481,9482,9484,9487,9489,9491,9493,9497,9501

# Calculate the distances and plot distribution
RDF_g GROUP 
ATOMS
the list of atoms which are involved the virtual atom's definition
=RDF_c1,RDF_c2,RDF_c3,RDF_c4,...,RDF_c285,RDF_c286,RDF_c287,RDF_c288
RDF_d DISTANCES GROUP=RDF_g MORE_THAN={RATIONAL R_0=0.01 D_0=2.09 D_MAX=2.09} HISTOGRAM={TRIANGULAR NBINS=208 BANDWIDTH=0.01 UPPER=2.09 LOWER=0.01}
PRINT ARG=RDF_d FILE=plumed_md_RDF.dat