One-dimesional flooding of the U5G truncated. The one collective variables are number of bonds following central hydrogen bonds at each bp along the helix axis multi RMSD folowing atoms for consecutive eta and thea psedotorsions. In this version the H-bonds of . All H-bonds are computed heavy atom to heavy atom. Changed the values so that restart files will be written five times. Also changed the max value and resolution to acquire extents between 150 and 200. Jason M. Imamoto, August 20, 2015 &cntrl imin=0, ntx=5, irest=1, ntxo=1, ntpr=2500, ntwr=-50000, ntwx=2500, ntwv=50000, ntwe=2500, ntf=2, ntc=2, ntb=1, nstlim=50000, dt=0.002, iwrap=1,ntr=0, nmropt=1, temp0=300.0, tempi=300.0, tautp=1.0, ntt=3, gamma_ln=1.0, ig=-1, ntp=0, pres0=1.0, comp=44.6, taup=0.2, tol=0.00005 &end &ewald order=4, ew_type=0 &end / ncsu_abmd mode = FLOODING monitor_file = 'bias/rs2_1DvA2.mon.2.txt' monitor_freq = 5000 umbrella_file = 'bias/rs2_1DvA2.bias.nc' timescale = 10.0 variable type = MULTI_RMSD i = (6, 29, 36, 60, 0, 60, 67, 94, 101, 0, 101, 127, 134, 161, 0, 161, 168, 191, 198, 0, 198, 224, 231, 255, 0, 292, 319, 326, 353, 0, 353, 360, 387, 394, 0, 394, 420, 427, 453, 0, 453, 460, 486, 493, 0 ) r = (37.911,52.796,33.165, 38.737,49.228,31.812, 42.646,48.597,32.723, 43.466,44.698,32.684, 43.466,44.698,32.684, 45.937,44.261,35.721, 45.375,40.556,36.676, 41.905,39.930,34.936, 41.905,39.930,34.936, 40.312,40.679,32.041, 38.496,37.922,34.064, 40.258,34.669,33.098, 40.258,34.669,33.098, 43.424,34.924,35.399, 43.627,31.651,37.437, 44.875,33.218,40.982, 44.875,33.218,40.982, 44.475,29.824,42.300, 42.081,30.030,45.232, 41.229,26.283,45.395, 26.513,28.895,36.597, 26.265,32.490,37.929, 27.610,32.923,41.769, 28.570,36.673,41.041, 28.570,36.673,41.041, 31.957,36.938,43.028, 33.583,40.202,42.268, 36.404,40.006,44.169, 36.404,40.006,44.169, 37.785,42.983,46.069, 40.924,41.965,48.285, 42.818,45.460,48.499, 42.818,45.460,48.499, 46.635,44.352,48.783, 48.066,47.781,48.674, 50.224,47.911,45.426) min = 0.0 max = 2.5 resolution = 0.10 ! required for mode = FLOODING end variable end ncsu_abmd / &wt TYPE='END' /