Project ID: plumID:19.061
Source: diffusion_meta.dat
Originally used with PLUMED version: 2.5
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

#Restart the simulation
RESTART

#Define the guest molecule in the simulation
guest: GROUP ATOMS=169-186
guest_com: COM ATOMS=guest

#Define the cage centre of mass
centre_com: COM ATOMS=1-168

#Define the centres of the windows as the centre of the three phenyl H atoms in the window
circle1: CENTER ATOMS=22,78,134
circle2: CENTER ATOMS=36,64,162
circle3: CENTER ATOMS=8,106,148
circle4: CENTER ATOMS=50,92,120

#Define distances between the guest centre of mass and the centres of the windows of interest
d1: DISTANCE ATOMS=guest_com,circle1
d2: DISTANCE ATOMS=guest_com,circle2

#Define distances that will need energetic walls - these are the distances to the other two windows and the overall distance from the cage centre of mass
d3: DISTANCE ATOMS=guest_com,circle3
d4: DISTANCE ATOMS=guest_com,circle4
dc: DISTANCE ATOMS=centre_com,guest_com

lwalls: LOWER_WALLS ARG=d3,d4 AT=0.25,0.25 KAPPA=4500,4500 OFFSET=0,0 EXP=2,2 EPS=1,1
uwall: UPPER_WALLS ARG=dc AT=0.45 KAPPA=3500 OFFSET=0 EXP=2 EPS=1

#Deposit Gaussians, with the distances d1 and d2 as the collective variable
meta: METAD ARG=d1,d2 SIGMA=0.01,0.01 HEIGHT=1.2 BIASFACTOR=15 TEMP=300 PACE=500 GRID_MIN=-2.0,-2.0 GRID_MAX=6.0,6.0 GRID_BIN=4000,4000 

PRINT ARG=d1,d2,d3,d4,meta.*,uwall.*,lwalls.* FILE=COLVAR STRIDE=2000