[gmx-users] Interpretation of g_chi results

[naimah haron naimah]

Dear All:

I saw in the manual that by g_chi the NMR and Jcoupling of the system can be calculated. But when I perform the command which is 
 Then I got these 2 output file which is:

g_chi -s cat125_md.gro -f cat125_md.xtc -o nmr.xvg -jc Jcoupling.xvg -shift 
 
@ title "Dihedral Order Parameters"
@ xaxis label "Residue"
@ yaxis label "S2"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "S2Min"
@ s1 legend "S2Max"
@ s2 legend "Phi"
@ s3 legend "Psi"
@ s4 legend "Omega"
#Res. S2Min S2Max Phi Psi Omega 
127 0.241 0.883 0.883 0.659 0.241 
128 0.241 0.793 0.440 0.793 0.241 
129 0.149 0.312 0.312 0.149 0.307 
130 0.020 0.624 0.624 0.196 0.020 
131 0.131 0.782 0.782 0.674 0.131 
132 0.015 0.865 0.865 0.015 0.463 
133 0.275 0.522 0.522 0.275 0.281 
134 0.262 0.801 0.801 0.262 0.300 
135 0.349 0.611 0.611 0.427 0.349 
136 0.383 0.799 0.799 0.383 0.565 
137 0.562 0.773 0.773 0.562 0.566 
138 0.216 0.810 0.810 0.545 0.216 
139 0.042 0.776 0.042 0.776 0.065 
140 0.319 0.783 0.783 0.319 0.508 
141 0.196 0.882 0.882 0.760 0.196 
142 0.658 0.731 0.731 0.724 0.658 
143 0.033 0.606 0.033 0.606 0.101 
144 0.202 0.888 0.888 0.587 0.202 
145 0.014 0.824 0.217 0.824 0.014 
146 0.236 0.862 0.862 0.236 0.437 
147 0.039 0.814 0.814 0.039 0.449 
148 0.087 0.766 0.766 0.425 0.087 
149 0.028 0.795 0.795 0.028 0.038 
150 0.195 0.952 0.952 0.816 0.195 
151 0.444 0.740 0.635 0.740 0.444 
152 0.155 0.903 0.903 0.155 0.245 
153 0.087 0.581 0.581 0.234 0.087 
154 0.010 0.775 0.775 0.128 0.010 
155 0.110 0.748 0.748 0.215 0.110 
156 0.252 0.618 0.618 0.252 0.299 
157 0.020 0.688 0.020 0.688 0.032 
158 0.285 0.757 0.757 0.285 0.396 
159 0.213 0.827 0.672 0.827 0.213 
160 0.023 0.438 0.438 0.023 0.270 
161 0.197 0.912 0.912 0.783 0.197 
162 0.040 0.368 0.368 0.040 0.095 
163 0.112 0.563 0.235 0.563 0.112 
164 0.207 0.666 0.666 0.207 0.610 
165 0.128 0.872 0.872 0.128 0.174 
166 0.024 0.281 0.096 0.281 0.024 
167 0.057 0.798 0.798 0.057 0.475 
168 0.210 0.821 0.821 0.296 0.210 
169 0.252 0.488 0.370 0.488 0.252 
170 0.610 0.723 0.723 0.717 0.610 
171 0.232 0.716 0.716 0.624 0.232 
172 0.102 0.892 0.892 0.102 0.215 
173 0.068 0.089 0.089 0.086 0.068 
174 0.450 0.899 0.899 0.827 0.450 
175 0.001 0.209 0.001 0.209 0.042 
176 0.139 0.528 0.528 0.140 0.139 
177 0.165 0.531 0.165 0.531 0.168 
178 0.194 0.662 0.662 0.285 0.194 
179 0.197 0.517 0.197 0.517 0.225 
180 0.144 0.470 0.470 0.239 0.144 
181 0.371 0.597 0.597 0.429 0.371 
182 0.603 0.909 0.909 0.881 0.603 
183 0.149 0.731 0.731 0.149 0.479 
184 0.233 0.845 0.845 0.707 0.233 
185 0.006 0.828 0.828 0.006 0.707 
186 0.142 0.682 0.582 0.682 0.142 
187 0.002 0.552 0.552 0.003 0.002 
188 0.331 0.637 0.601 0.637 0.331 
189 0.477 0.787 0.609 0.787 0.477 
190 0.030 0.284 0.251 0.030 0.284 
191 0.371 0.868 0.868 0.772 0.371 
192 0.227 0.957 0.957 0.227 0.443 
193 0.005 0.409 0.409 0.228 0.005 
194 0.224 0.780 0.561 0.780 0.224 
195 0.678 0.845 0.830 0.845 0.678 
196 0.206 0.307 0.283 0.206 0.307 
197 0.141 0.856 0.856 0.286 0.141 
198 0.313 0.649 0.435 0.649 0.313 
199 0.019 0.048 0.019 0.048 0.027 
200 0.055 0.805 0.805 0.055 0.347 
201 0.073 0.334 0.073 0.334 0.103 
202 0.217 0.648 0.602 0.648 0.217 
203 0.040 0.622 0.622 0.349 0.040 
204 0.017 0.838 0.017 0.838 0.117 
205 0.024 0.192 0.024 0.192 0.043 
206 0.006 0.785 0.006 0.785 0.459 
207 0.158 0.172 0.158 0.167 0.172 
208 0.479 0.751 0.732 0.751 0.479 
209 0.328 0.925 0.925 0.855 0.328 
210 0.325 0.589 0.589 0.325 0.507 
211 0.495 0.944 0.944 0.680 0.495 
212 0.127 0.689 0.689 0.127 0.513 
213 0.385 0.899 0.899 0.858 0.385 
214 0.181 0.417 0.181 0.198 0.417 
215 0.199 0.832 0.832 0.757 0.199 
216 0.479 0.836 0.836 0.771 0.479 
217 0.787 0.860 0.860 0.787 0.817 
218 0.174 0.887 0.887 0.174 0.318 
219 0.321 0.837 0.837 0.561 0.321 
220 0.141 0.186 0.152 0.141 0.186 
221 0.104 0.864 0.783 0.864 0.104 
222 0.245 0.371 0.288 0.245 0.371 
223 0.035 0.363 0.198 0.035 0.363 
224 0.013 0.823 0.013 0.823 0.110 
225 0.020 0.897 0.897 0.020 0.787 
226 0.269 0.821 0.779 0.821 0.269 
227 0.101 0.846 0.175 0.846 0.101 
228 0.218 0.412 0.358 0.412 0.218 
229 0.259 0.750 0.601 0.750 0.259 
230 0.671 0.901 0.685 0.901 0.671 
231 0.267 0.340 0.340 0.276 0.267 
232 0.070 0.869 0.070 0.869 0.158 
233 0.534 0.902 0.902 0.839 0.534 
234 0.009 0.280 0.009 0.280 0.096 
235 0.103 0.765 0.630 0.765 0.103 
236 0.130 0.172 0.172 0.157 0.130 
237 0.214 0.869 0.869 0.214 0.246 
238 0.111 0.707 0.707 0.467 0.111 
239 0.338 0.682 0.682 0.576 0.338 
240 0.460 0.936 0.936 0.833 0.460 
241 0.854 0.942 0.942 0.862 0.854 
242 0.592 0.827 0.827 0.771 0.592 
243 0.118 0.717 0.717 0.118 0.529 
244 0.549 0.719 0.719 0.631 0.549 
245 0.066 0.660 0.660 0.066 0.297 
246 0.205 0.867 0.867 0.205 0.585 
247 0.029 0.176 0.046 0.176 0.029 
248 0.092 0.782 0.092 0.782 0.222 
249 0.141 0.341 0.164 0.341 0.141 
250 0.061 0.699 0.699 0.061 0.491 
 
 
 @ title "\S3\NJ-Couplings from Karplus Equation"
@ xaxis label "Residue"
@ yaxis label "Coupling"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "J_NHa"
@ s1 legend "J_HaC'"
@ s2 legend "J_NHCb"
@ s3 legend "J_Ci-1Hai"
@ s4 legend "J_HaN"
@ s5 legend "JHaHb2"
@ s6 legend "JHaHb3"
#Res. J_NHa J_HaC' J_NHCb J_Ci-1Hai J_HaN JHaHb2 JHaHb3 
127 2.738  0.812 5.396 0.703 -0.615 0.000 0.000
128 6.686 1.739 1.175 0.650 -0.714 0.000 0.000
129 4.360 2.977 1.561 2.100 -0.838 0.000 0.000
130 7.197 1.005 1.583 1.017 -0.369 0.000 0.000
131 4.079 4.118 0.310 2.126 -0.607 0.000 0.000
132 2.207 1.829 4.550 -0.717 -0.650 0.000 0.000
133 3.642 0.656 4.881 1.304 -0.426 0.000 0.000
134 4.814 3.513 0.551 3.048 -0.606 0.000 0.000
135 5.758 1.910 1.744 0.228 -0.577 0.000 0.000
136 2.819 4.361 0.884 0.802 -0.962 0.000 0.000
137 4.843 2.296 2.010 -0.071 -0.375 0.000 0.000
138 2.784 4.509 0.710 0.511 -0.323 0.000 0.000
139 5.410 2.086 1.778 1.919 -0.518 0.000 0.000
140 2.824 3.710 1.575 -0.186 -0.347 0.000 0.000
141 2.434 1.038 5.346 0.219 -0.476 0.000 0.000
142 3.390 0.738 4.993 1.479 -0.324 0.000 0.000
143 5.025 2.013 2.090 0.925 -0.378 0.000 0.000
144 7.412 2.055 0.346 0.806 -0.468 0.000 0.000
145 3.878 2.934 1.862 1.239 -0.682 0.000 0.000
146 4.724 3.681 0.405 2.987 -1.001 0.000 0.000
147 5.350 2.496 1.408 3.620 -0.421 0.000 0.000
148 8.166 0.768 1.193 1.158 -0.489 0.000 0.000
149 2.591 4.064 1.342 -0.074 -0.379 0.000 0.000
150 2.427 4.983 0.419 0.537 -0.646 0.000 0.000
151 3.135 3.220 1.945 0.094 -1.143 0.000 0.000
152 8.602 1.482 0.113 1.377 -0.579 0.000 0.000
153 4.079 1.634 3.365 0.013 -0.364 0.000 0.000
154 7.442 1.737 0.678 0.847 -0.666 0.000 0.000
155 4.959 2.830 1.276 3.203 -0.791 0.000 0.000
156 5.190 1.609 2.577 3.257 -0.590 0.000 0.000
157 4.271 1.911 2.787 0.877 -0.538 0.000 0.000
158 2.336 3.905 1.705 -0.429 -0.564 0.000 0.000
159 7.579 1.494 0.850 0.999 -0.319 0.000 0.000
160 7.044 0.836 1.932 1.028 -0.553 0.000 0.000
161 2.648 2.400 3.536 -0.944 -0.264 0.000 0.000
162 6.340 1.663 1.553 0.628 -0.399 0.000 0.000
163 4.908 1.591 2.800 2.209 -0.369 0.000 0.000
164 5.668 1.630 1.936 0.363 -0.528 0.000 0.000
165 4.868 1.520 2.617 -0.323 -0.543 0.000 0.000
166 4.401 1.838 2.831 1.508 -0.751 0.000 0.000
167 2.505 1.133 5.176 0.417 -0.360 0.000 0.000
168 2.267 1.458 4.953 -0.321 -0.375 0.000 0.000
169 5.992 1.550 2.004 0.806 -0.293 0.000 0.000
170 4.515 1.196 3.619 2.760 -0.308 0.000 0.000
171 6.448 1.003 2.116 0.377 -0.936 0.000 0.000
172 8.031 0.335 1.752 1.092 -0.341 0.000 0.000
173 4.849 2.618 1.579 1.793 -0.641 0.000 0.000
174 2.612 0.828 5.470 0.568 -0.741 0.000 0.000
175 4.101 1.777 3.079 0.533 -0.381 0.000 0.000
176 6.619 0.853 2.193 0.752 -0.718 0.000 0.000
177 3.671 1.365 3.956 0.667 -0.935 0.000 0.000
178 4.519 0.904 3.965 2.496 -0.360 0.000 0.000
179 5.901 2.545 0.934 2.886 -0.331 0.000 0.000
180 5.186 2.433 1.579 0.366 -0.461 0.000 0.000
181 6.208 0.693 2.663 0.488 -1.138 0.000 0.000
182 7.311 0.473 2.093 0.770 -0.440 0.000 0.000
183 2.835 1.665 4.274 -0.339 -0.463 0.000 0.000
184 3.629 4.396 0.298 1.804 -0.405 0.000 0.000
185 4.197 0.559 4.623 2.495 -0.531 0.000 0.000
186 6.713 1.619 1.381 0.809 -0.579 0.000 0.000
187 4.467 1.810 2.851 -0.022 -0.509 0.000 0.000
188 6.770 0.571 2.415 0.617 -0.468 0.000 0.000
189 6.868 0.881 1.982 0.653 -0.311 0.000 0.000
190 4.827 2.197 1.951 0.633 -0.512 0.000 0.000
191 2.602 4.669 0.666 0.599 -0.468 0.000 0.000
192 2.207 2.407 3.859 -1.108 -0.580 0.000 0.000
193 3.999 3.275 1.310 1.057 -0.635 0.000 0.000
194 5.814 1.584 1.901 0.480 -0.716 0.000 0.000
195 6.672 0.835 2.137 0.430 -0.702 0.000 0.000
196 3.627 3.495 1.336 0.727 -0.469 0.000 0.000
197 8.859 0.799 0.669 1.489 -0.399 0.000 0.000
198 6.952 1.152 1.645 0.876 -0.819 0.000 0.000
199 4.413 1.932 2.656 0.407 -0.454 0.000 0.000
200 8.417 1.271 0.496 1.365 -0.354 0.000 0.000
201 5.990 1.195 2.345 1.196 -0.484 0.000 0.000
202 5.321 2.936 0.861 3.141 -0.374 0.000 0.000
203 7.414 1.411 1.082 1.015 -0.727 0.000 0.000
204 2.916 3.297 2.145 -0.013 -0.671 0.000 0.000
205 5.700 1.964 1.669 1.564 -0.662 0.000 0.000
206 6.136 2.036 1.284 1.781 -0.801 0.000 0.000
207 3.755 1.941 3.204 0.323 -0.395 0.000 0.000
208 2.982 3.169 2.090 -0.308 -0.516 0.000 0.000
209 5.947 2.192 1.354 4.210 -0.654 0.000 0.000
210 5.033 1.802 2.471 3.104 -0.369 0.000 0.000
211 1.938 4.893 0.852 -0.129 -0.336 0.000 0.000
212 4.717 2.126 2.294 -0.116 -0.446 0.000 0.000
213 2.103 4.668 1.001 -0.020 -0.363 0.000 0.000
214 5.936 1.533 1.998 0.747 -0.846 0.000 0.000
215 5.606 2.427 1.268 0.026 -0.613 0.000 0.000
216 4.131 0.619 4.605 2.358 -0.722 0.000 0.000
217 2.565 1.054 5.232 0.413 -0.639 0.000 0.000
218 4.775 2.636 1.652 -0.333 -0.407 0.000 0.000
219 7.130 2.049 0.558 0.675 -0.581 0.000 0.000
220 4.181 3.160 1.305 0.116 -0.575 0.000 0.000
221 5.255 2.579 1.372 3.499 -0.256 0.000 0.000
222 3.658 1.730 3.510 1.569 -0.509 0.000 0.000
223 5.612 1.466 2.414 1.331 -0.656 0.000 0.000
224 2.366 2.702 3.251 -0.809 -0.362 0.000 0.000
225 5.846 1.003 2.518 0.070 -0.598 0.000 0.000
226 4.889 3.186 0.885 3.095 -0.837 0.000 0.000
227 4.410 2.708 1.794 1.776 -0.600 0.000 0.000
228 4.447 1.077 3.756 0.808 -0.402 0.000 0.000
229 6.669 0.574 2.481 0.581 -0.664 0.000 0.000
230 4.543 3.062 1.308 -0.349 -0.592 0.000 0.000
231 5.481 2.179 1.670 2.945 -0.357 0.000 0.000
232 3.358 1.874 3.443 -0.117 -0.617 0.000 0.000
233 5.518 2.913 0.781 3.798 -0.566 0.000 0.000
234 4.332 2.280 2.300 0.466 -0.574 0.000 0.000
235 7.574 1.105 1.248 0.936 -0.668 0.000 0.000
236 5.572 1.067 2.883 1.011 -0.885 0.000 0.000
237 4.828 3.574 0.467 3.123 -0.466 0.000 0.000
238 6.403 1.971 1.191 0.429 -0.364 0.000 0.000
239 4.550 2.120 2.425 -0.188 -0.664 0.000 0.000
240 5.813 2.598 0.957 4.096 -0.706 0.000 0.000
241 3.360 2.367 2.709 -0.884 -0.516 0.000 0.000
242 7.158 1.997 0.601 0.725 -0.616 0.000 0.000
243 3.885 4.236 0.312 1.921 -0.649 0.000 0.000
244 7.853 0.897 1.278 0.998 -0.849 0.000 0.000
245 4.477 2.822 1.620 2.708 -0.723 0.000 0.000
246 5.469 2.529 1.255 -0.040 -0.668 0.000 0.000
247 2.905 3.159 2.354 0.197 -0.540 0.000 0.000
248 5.566 1.784 2.065 1.612 -0.290 0.000 0.000
249 5.790 1.456 2.153 0.789 -0.350 0.000 0.000
250 4.869 1.207 3.326 3.106 -0.791 0.000 0.000
 
 
My question is what the value should be for the NMR and Jcoupling? Does anyone knows how to calculate the NMR of the simulated system ?
 
Thanks for the comments.


NAIMAH HARON
DEPARTMENT OF CHEMISTRY,
FACULTY OF SCIENCE,
UNIVERSITY PUTRA MALAYSIA,
MALAYSIA.


      
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