> > I am trying to get an rdf graph actually, and my values are very close > to one, but not exactly one, and I was wondering if there is some > normalization issue with g_rdf? These are my values for rdf: > > 0 0 > 0.002 0 > 0.004 0 > 0.006 0 > 0.008 0 > 0.01 0 > 0.012 0 > 0.014 0 > 0.016 0 > 0.018 0 > 0.02 0 > 0.022 0 > 0.024 0 > 0.026 0 > 0.028 0 > 0.03 0 > 0.032 0 > 0.034 0 > 0.036 0 > 0.038 0 > 0.04 0 > 0.042 0 > 0.044 0 > 0.046 0 > 0.048 0 > 0.05 0 > 0.052 0 > 0.054 0 > 0.056 0 > 0.058 0 > 0.06 0 > 0.062 0 > 0.064 0 > 0.066 0 > 0.068 0 > 0.07 0 > 0.072 0 > 0.074 0 > 0.076 0 > 0.078 0 > 0.08 0 > 0.082 0 > 0.084 0 > 0.086 0 > 0.088 0 > 0.09 0 > 0.092 0 > 0.094 0 > 0.096 0 > 0.098 0 > 0.1 0 > 0.102 0 > 0.104 0 > 0.106 0 > 0.108 0 > 0.11 0 > 0.112 0 > 0.114 0 > 0.116 0 > 0.118 0 > 0.12 0 > 0.122 0 > 0.124 0 > 0.126 0 > 0.128 0 > 0.13 0 > 0.132 0 > 0.134 0 > 0.136 0 > 0.138 0 > 0.14 0 > 0.142 0 > 0.144 0 > 0.146 0 > 0.148 0 > 0.15 0 > 0.152 0 > 0.154 0 > 0.156 0 > 0.158 0 > 0.16 0 > 0.162 0 > 0.164 0 > 0.166 0 > 0.168 0 > 0.17 0 > 0.172 0 > 0.174 0 > 0.176 0 > 0.178 0 > 0.18 0 > 0.182 0 > 0.184 0 > 0.186 0 > 0.188 0 > 0.19 0 > 0.192 0 > 0.194 0 > 0.196 0 > 0.198 0 > 0.2 0 > 0.202 0 > 0.204 0 > 0.206 0 > 0.208 0 > 0.21 0 > 0.212 0 > 0.214 0 > 0.216 0 > 0.218 0 > 0.22 0 > 0.222 0 > 0.224 0 > 0.226 0 > 0.228 0 > 0.23 0 > 0.232 0 > 0.234 0 > 0.236 0 > 0.238 0 > 0.24 0 > 0.242 0 > 0.244 0 > 0.246 0 > 0.248 0 > 0.25 0 > 0.252 0 > 0.254 0 > 0.256 0 > 0.258 0 > 0.26 0 > 0.262 0 > 0.264 0 > 0.266 0 > 0.268 3.32195e-05 > 0.27 3.27293e-05 > 0.272 0.000193501 > 0.274 0.000317806 > 0.276 0.000689078 > 0.278 0.00126578 > 0.28 0.00197816 > 0.282 0.00348035 > 0.284 0.00653762 > 0.286 0.0111138 > 0.288 0.016713 > 0.29 0.0238596 > 0.292 0.0345034 > 0.294 0.0528889 > 0.296 0.0698775 > 0.298 0.0933922 > 0.3 0.118079 > 0.302 0.156417 > 0.304 0.195336 > 0.306 0.242149 > 0.308 0.287833 > 0.31 0.351093 > 0.312 0.411434 > 0.314 0.473243 > 0.316 0.538749 > 0.318 0.61093 > 0.32 0.688108 > 0.322 0.756748 > 0.324 0.837504 > 0.326 0.914596 > 0.328 0.993652 > 0.33 1.0663 > 0.332 1.13958 > 0.334 1.21522 > 0.336 1.29358 > 0.338 1.35543 > 0.34 1.42607 > 0.342 1.49061 > 0.344 1.54496 > 0.346 1.59492 > 0.348 1.64578 > 0.35 1.6887 > 0.352 1.73861 > 0.354 1.7676 > 0.356 1.78996 > 0.358 1.82775 > 0.36 1.83798 > 0.362 1.84435 > 0.364 1.85567 > 0.366 1.86664 > 0.368 1.87024 > 0.37 1.86585 > 0.372 1.85472 > 0.374 1.84964 > 0.376 1.84624 > 0.378 1.82577 > 0.38 1.8069 > 0.382 1.78844 > 0.384 1.77257 > 0.386 1.75025 > 0.388 1.72797 > 0.39 1.69894 > 0.392 1.67908 > 0.394 1.6537 > 0.396 1.62812 > 0.398 1.60552 > 0.4 1.57759 > 0.402 1.55621 > 0.404 1.53355 > 0.406 1.49578 > 0.408 1.48583 > 0.41 1.45567 > 0.412 1.43467 > 0.414 1.41543 > 0.416 1.3816 > 0.418 1.36369 > 0.42 1.34185 > 0.422 1.31562 > 0.424 1.28986 > 0.426 1.27127 > 0.428 1.24739 > 0.43 1.23036 > 0.432 1.21598 > 0.434 1.20053 > 0.436 1.17903 > 0.438 1.1627 > 0.44 1.1486 > 0.442 1.12971 > 0.444 1.10987 > 0.446 1.10068 > 0.448 1.08301 > 0.45 1.06589 > 0.452 1.0572 > 0.454 1.03356 > 0.456 1.02144 > 0.458 1.01093 > 0.46 0.999176 > 0.462 0.983748 > 0.464 0.976315 > 0.466 0.960132 > 0.468 0.95193 > 0.47 0.940119 > 0.472 0.937507 > 0.474 0.92746 > 0.476 0.91218 > 0.478 0.905227 > 0.48 0.901027 > 0.482 0.883861 > 0.484 0.872012 > 0.486 0.871501 > 0.488 0.861236 > 0.49 0.855628 > 0.492 0.85084 > 0.494 0.846611 > 0.496 0.839804 > 0.498 0.832431 > 0.5 0.82711 > 0.502 0.820518 > 0.504 0.815931 > 0.506 0.805553 > 0.508 0.809657 > 0.51 0.802229 > 0.512 0.799135 > 0.514 0.794028 > 0.516 0.7938 > 0.518 0.789457 > 0.52 0.787434 > 0.522 0.785199 > 0.524 0.780233 > 0.526 0.777301 > 0.528 0.7782 > 0.53 0.780274 > 0.532 0.78405 > 0.534 0.779049 > 0.536 0.778457 > 0.538 0.777937 > 0.54 0.788429 > 0.542 0.781973 > 0.544 0.782796 > 0.546 0.788838 > 0.548 0.791638 > 0.55 0.794149 > 0.552 0.797927 > 0.554 0.799896 > 0.556 0.806044 > 0.558 0.806472 > 0.56 0.815236 > 0.562 0.822147 > 0.564 0.824565 > 0.566 0.82688 > 0.568 0.837779 > 0.57 0.839535 > 0.572 0.85107 > 0.574 0.859169 > 0.576 0.865325 > 0.578 0.876879 > 0.58 0.881985 > 0.582 0.89474 > 0.584 0.893694 > 0.586 0.904503 > 0.588 0.920122 > 0.59 0.930537 > 0.592 0.934759 > 0.594 0.946158 > 0.596 0.951872 > 0.598 0.962671 > 0.6 0.968691 > 0.602 0.976406 > 0.604 0.989538 > 0.606 0.994007 > 0.608 1.0051 > 0.61 1.01191 > 0.612 1.01618 > 0.614 1.02365 > 0.616 1.03378 > 0.618 1.0341 > 0.62 1.04287 > 0.622 1.04814 > 0.624 1.05048 > 0.626 1.05958 > 0.628 1.06044 > 0.63 1.0703 > 0.632 1.06911 > 0.634 1.07214 > 0.636 1.07062 > 0.638 1.07816 > 0.64 1.07716 > 0.642 1.07854 > 0.644 1.07833 > 0.646 1.08024 > 0.648 1.08212 > 0.65 1.07849 > 0.652 1.07939 > 0.654 1.08222 > 0.656 1.08643 > 0.658 1.07989 > 0.66 1.08555 > 0.662 1.0809 > 0.664 1.07697 > 0.666 1.07408 > 0.668 1.07359 > 0.67 1.07393 > 0.672 1.07496 > 0.674 1.07261 > 0.676 1.06707 > 0.678 1.06585 > 0.68 1.06882 > 0.682 1.06825 > 0.684 1.06476 > 0.686 1.06102 > 0.688 1.0595 > 0.69 1.05802 > 0.692 1.05431 > 0.694 1.0556 > 0.696 1.05047 > 0.698 1.04914 > 0.7 1.04683 > 0.702 1.04544 > 0.704 1.04485 > 0.706 1.04227 > 0.708 1.04364 > 0.71 1.03773 > 0.712 1.03028 > 0.714 1.03173 > 0.716 1.0344 > 0.718 1.03129 > 0.72 1.03139 > 0.722 1.02722 > 0.724 1.02874 > 0.726 1.02073 > 0.728 1.02168 > 0.73 1.01921 > 0.732 1.01825 > 0.734 1.02057 > 0.736 1.01212 > 0.738 1.01283 > 0.74 1.01244 > 0.742 1.01218 > 0.744 1.0121 > 0.746 1.00697 > 0.748 1.00879 > 0.75 1.0049 > 0.752 1.00385 > 0.754 1.00454 > 0.756 1.00467 > 0.758 1.00241 > 0.76 1.00597 > 0.762 0.99878 > 0.764 0.999362 > 0.766 0.997916 > 0.768 0.999553 > 0.77 0.99394 > 0.772 0.996918 > 0.774 0.99861 > 0.776 0.998062 > 0.778 0.995829 > 0.78 0.995665 > 0.782 0.991158 > 0.784 0.993166 > 0.786 0.993317 > 0.788 0.988298 > 0.79 0.992643 > 0.792 0.991056 > 0.794 0.987305 > 0.796 0.98944 > 0.798 0.989074 > 0.8 0.986717 > 0.802 0.9882 > 0.804 0.98571 > 0.806 0.987209 > 0.808 0.990424 > 0.81 0.987083 > 0.812 0.985193 > 0.814 0.985061 > 0.816 0.984737 > 0.818 0.984942 > 0.82 0.984881 > 0.822 0.985885 > 0.824 0.987107 > 0.826 0.982715 > 0.828 0.985119 > 0.83 0.987138 > 0.832 0.985964 > 0.834 0.986005 > 0.836 0.981673 > 0.838 0.982415 > 0.84 0.984552 > 0.842 0.985368 > 0.844 0.977779 > 0.846 0.980927 > 0.848 0.984628 > 0.85 0.989775 > 0.852 0.986042 > 0.854 0.984692 > 0.856 0.985441 > 0.858 0.986366 > 0.86 0.985887 > 0.862 0.98888 > 0.864 0.988611 > 0.866 0.989229 > 0.868 0.986269 > 0.87 0.987912 > 0.872 0.986648 > 0.874 0.990954 > 0.876 0.989813 > 0.878 0.990742 > 0.88 0.990515 > 0.882 0.986976 > 0.884 0.993526 > 0.886 0.991169 > 0.888 0.992141 > 0.89 0.990366 > 0.892 0.9913 > 0.894 0.995312 > 0.896 0.990771 > 0.898 0.992455 > 0.9 0.991514 > 0.902 0.993262 > 0.904 0.996755 > 0.906 0.995517 > 0.908 0.996353 > 0.91 0.991881 > 0.912 0.994453 > 0.914 0.995881 > 0.916 0.995968 > 0.918 0.998059 > 0.92 0.995915 > 0.922 0.996393 > 0.924 0.997279 > 0.926 0.997195 > 0.928 0.996136 > 0.93 0.999274 > 0.932 0.995831 > 0.934 0.995949 > 0.936 1.00109 > 0.938 0.998608 > 0.94 0.997568 > 0.942 1.00137 > 0.944 1.0007 > 0.946 1.0009 > 0.948 0.996415 > 0.95 1.0003 > 0.952 1.00409 > 0.954 1.00338 > 0.956 1.00173 > 0.958 1.00215 > 0.96 1.00346 > 0.962 1.0028 > 0.964 1.00146 > 0.966 1.00462 > 0.968 1.00401 > 0.97 1.00338 > 0.972 1.00557 > 0.974 1.00318 > 0.976 1.00616 > 0.978 1.00645 > 0.98 1.00794 > 0.982 1.00694 > 0.984 1.0042 > 0.986 1.00686 > 0.988 1.00617 > 0.99 1.0056 > 0.992 1.00399 > 0.994 1.00842 > 0.996 1.00801 > 0.998 1.00884 > 1 1.00467 > 1.002 1.00578 > 1.004 1.00838 > 1.006 1.0044 > 1.008 1.00527 > 1.01 1.00743 > 1.012 1.00738 > 1.014 1.00649 > 1.016 1.00986 > 1.018 1.00583 > 1.02 1.00782 > 1.022 1.00798 > 1.024 1.00568 > 1.026 1.00459 > 1.028 1.00885 > 1.03 1.00609 > 1.032 1.00694 > 1.034 1.00714 > 1.036 1.00495 > 1.038 1.00817 > 1.04 1.00915 > 1.042 1.00513 > 1.044 1.00798 > 1.046 1.00685 > 1.048 1.00411 > 1.05 1.0045 > 1.052 1.00475 > 1.054 1.00435 > 1.056 1.00723 > 1.058 1.00394 > 1.06 1.00548 > 1.062 1.00442 > 1.064 1.00523 > 1.066 1.00119 > 1.068 1.005 > 1.07 1.00338 > 1.072 1.00677 > 1.074 1.0056 > 1.076 1.00191 > 1.078 1.00364 > 1.08 1.00201 > 1.082 1.00091 > 1.084 1.00444 > 1.086 1.00395 > 1.088 1.00019 > 1.09 1.00312 > 1.092 1.00105 > 1.094 1.00046 > 1.096 1.00009 > 1.098 1.00238 > 1.1 0.997774 > 1.102 1.00116 > 1.104 0.999177 > 1.106 0.999075 > 1.108 0.99965 > 1.11 1.00027 > 1.112 0.996616 > 1.114 0.999098 > 1.116 0.999091 > 1.118 0.997033 > 1.12 0.999598 > 1.122 0.999695 > 1.124 0.998096 > 1.126 0.998339 > 1.128 0.997582 > 1.13 0.998625 > 1.132 0.996005 > 1.134 1.00085 > 1.136 0.998892 > 1.138 0.998049 > 1.14 0.997158 > 1.142 0.997571 > 1.144 0.999554 > 1.146 0.996233 > 1.148 1.00116 > 1.15 0.998207 > 1.152 0.998212 > 1.154 0.998348 > 1.156 0.996611 > 1.158 0.997155 > 1.16 0.995056 > 1.162 0.995144 > 1.164 0.996621 > 1.166 0.999163 > 1.168 0.994951 > 1.17 0.997941 > 1.172 0.997855 > 1.174 0.997045 > 1.176 0.996823 > 1.178 0.996131 > 1.18 0.996537 > 1.182 0.997731 > 1.184 0.996762 > 1.186 1.00028 > 1.188 1.00151 > 1.19 0.996905 > 1.192 0.998277 > 1.194 0.998658 > 1.196 0.997687 > 1.198 0.998443 > 1.2 0.998217 > 1.202 0.998213 > 1.204 0.997245 > 1.206 0.999272 > 1.208 0.995826 > 1.21 0.998851 > 1.212 0.998046 > 1.214 0.997038 > 1.216 0.998801 > 1.218 0.998077 > 1.22 0.998735 > 1.222 1.00081 > 1.224 1.00086 > 1.226 0.998978 > 1.228 0.997882 > 1.23 1.00016 > 1.232 1.00034 > 1.234 0.999402 > 1.236 0.999584 > 1.238 0.998325 > 1.24 0.998195 > 1.242 0.999467 > 1.244 0.999988 > 1.246 0.999602 > 1.248 1.001 > 1.25 1.0017 > 1.252 1.00054 > 1.254 1.00049 > 1.256 1.00116 > 1.258 1.00127 > 1.26 1.00187 > 1.262 1.0013 > 1.264 1.00039 > 1.266 1.00169 > 1.268 1.00177 > 1.27 1.0021 > 1.272 1.00309 > 1.274 1.00321 > 1.276 1.00184 > 1.278 1.00126 > 1.28 1.00054 > 1.282 0.999957 > 1.284 1.00404 > 1.286 1.00117 > 1.288 1.00093 > 1.29 1.00401 > 1.292 1.00123 > 1.294 1.00174 > 1.296 1.0012 > 1.298 1.00145 > 1.3 1.0011 > 1.302 1.00058 > 1.304 1.00468 > 1.306 1.00386 > 1.308 1.0001 > 1.31 1.00268 > 1.312 1.00259 > 1.314 1.00207 > 1.316 1.00328 > 1.318 1.00197 > 1.32 1.00273 > 1.322 1.00324 > 1.324 0.999678 > 1.326 0.999545 > 1.328 1.00222 > 1.33 1.00195 > 1.332 0.999959 > 1.334 1.00205 > 1.336 1.00177 > 1.338 1.00262 > 1.34 1.00283 > 1.342 1.00122 > 1.344 1.0023 > 1.346 1.00139 > 1.348 1.00301 > 1.35 1.00127 > 1.352 1.00175 > 1.354 1.00334 > 1.356 1.0008 > 1.358 1.0003 > 1.36 1.00191 > 1.362 1.00233 > 1.364 1.00145 > 1.366 1.00262 > 1.368 1.00097 > 1.37 1.00153 > 1.372 0.999986 > 1.374 1.00143 > 1.376 1.00064 > 1.378 1.00249 > 1.38 1.00159 > 1.382 1.00047 > 1.384 0.999746 > 1.386 1.00118 > 1.388 0.999218 > 1.39 0.999708 > 1.392 1.00165 > 1.394 1.00004 > 1.396 0.999487 > 1.398 0.999952 > 1.4 1.00119 > 1.402 1.00174 > 1.404 1.00025 > 1.406 1.0022 > 1.408 0.999813 > 1.41 0.999993 > 1.412 1.00085 > 1.414 1.00179 > 1.416 0.999285 > 1.418 1.0006 > 1.42 1.00155 > 1.422 1.00152 > 1.424 0.999442 > 1.426 0.999406 > 1.428 1.00012 > 1.43 1.0008 > 1.432 0.999421 > 1.434 0.999454 > 1.436 0.999732 > 1.438 1.00037 > 1.44 1.00073 > 1.442 0.999739 > 1.444 1.00011 > 1.446 0.999256 > 1.448 1.0008 > 1.45 1.00002 > 1.452 1.00107 > 1.454 1.00038 > 1.456 0.999125 > 1.458 1.00215 > 1.46 0.999675 > 1.462 1 > 1.464 0.999633 > 1.466 1.00094 > 1.468 1.00111 > 1.47 0.999618 > 1.472 0.998297 > 1.474 0.999693 > 1.476 1.00042 > 1.478 1.00028 > 1.48 1.00272 > 1.482 1.00026 > > Near the end, the values are fluctuating around one. The reason I was > trying to get density values was may be to try an understand if the > density computed by gromacs is different for just water system and > water+one methane system (i.e. gromacs calculates the density using > the box and total number of molecules in the box, which would be fine > for water system but for methane+water it would slightly be a little > different, no?) and may be normalize my rdf using the difference in > the density factor. Does that make sense? > > -Nisha
If you don't use barostat, the density of the system is fixed by yourself. g_rdf uses it to calculate the average particle density in the box. Your rdf seems very reasonable as for me. This is another question how you selected the concrete value for methane in water system... -- Dr. Vitaly Chaban
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