Re: [gmx-users] umbrella sample Question
Thanks Justin, You are right. Your script might not be compatible with my system or software, I tried to use another python script from other people and showed a complete dat file. Thanks again Yours, Liu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] umbrella sample Question
On 8/18/17 10:28 PM, yujie liu wrote: Thanks Justin, What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate the distance from all confxxx.gro as well as your script and just didn’t extract the distance value completely to a text. Can I use a fast method to extract these value? That's what my script intends to do. Nothing I have on hand reproduces a problem, but clearly something is up with the parsing. You'll either have to diagnose what's going on with my script or write your own. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] umbrella sample Question
Hi, This happens to me also for a long time and could not find any solution. There are no error messages coming when we execute the gmx distance. I ran the script multiple time to get a full set of distance data and execute the command separately for the missing one. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] umbrella sample Question
Thanks Justin, What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate the distance from all confxxx.gro as well as your script and just didn’t extract the distance value completely to a text. Can I use a fast method to extract these value? Please look my summary_distances.dat file -- 0 0.507 1 0.499 2 0.500 3 0.512 4 0.505 5 0.497 6 0.516 7 0.499 8 0.509 9 0.506 10 0.510 11 0.508 12 0.504 13 0.513 14 0.505 15 0.506 16 0.502 17 0.506 18 0.505 19 0.498 20 0.506 21 0.501 22 0.501 23 0.503 24 0.510 25 0.503 26 0.507 27 0.510 28 0.504 29 0.516 30 0.516 31 0.511 32 0.515 33 0.516 34 0.519 35 0.517 36 0.514 37 0.517 38 0.515 39 0.517 40 0.509 41 0.514 42 0.517 43 0.520 44 0.508 45 0.522 46 0.519 47 0.517 48 0.510 49 0.503 50 0.515 51 0.506 52 0.507 53 0.507 54 0.503 55 0.516 56 0.524 57 0.506 58 0.522 59 0.510 60 0.510 61 0.523 62 0.517 63 0.512 64 0.512 65 0.502 66 0.517 67 0.515 68 0.522 69 0.512 70 0.509 71 0.511 72 0.512 73 0.515 74 75 0.507 76 0.514 77 0.515 78 0.515 79 0.508 80 0.512 81 0.515 82 0.512 83 0.521 84 0.523 85 0.525 86 0.521 87 0.526 88 0.529 89 0.539 90 0.532 91 0.530 92 0.525 93 0.528 94 0.540 95 0.538 96 0.531 97 0.532 98 99 0.536 100 0.543 101 0.531 102 0.550 103 0.542 104 105 0.534 106 0.537 107 0.547 108 0.542 109 0.547 110 0.550 111 0.562 112 0.572 113 0.575 114 0.573 115 0.569 116 0.586 117 0.586 118 0.568 119 0.583 120 0.580 121 0.600 122 123 0.583 124 0.578 125 0.593 126 0.587 127 0.595 128 0.611 129 130 0.616 131 132 0.623 133 0.622 134 0.629 135 0.633 136 0.633 137 0.648 138 0.640 139 0.633 140 0.643 141 0.630 142 0.636 143 0.651 144 145 0.665 146 0.685 147 148 0.697 149 0.724 150 0.728 151 152 0.732 153 0.753 154 0.757 155 0.760 156 0.758 157 0.765 158 0.783 159 0.799 160 161 0.865 162 163 0.877 164 0.883 165 0.887 166 167 0.914 168 0.917 169 170 171 0.942 172 0.955 173 0.986 174 0.993 175 0.989 176 1.018 177 1.048 178 179 1.067 180 181 182 183 184 1.132 185 1.119 186 1.127 187 188 189 190 1.237 191 192 1.289 193 1.347 194 195 196 1.395 197 1.432 198 199 200 201 1.719 202 203 1.828 204 205 1.961 206 1.980 207 208 209 210 2.089 211 2.111 212 2.114 213 2.152 214 2.168 215 216 217 2.217 218 2.214 219 2.239 220 2.271 221 222 223 224 225 226 227 228 2.489 229 230 2.536 231 2.553 232 233 2.625 234 2.667 235 2.692 236 2.693 237 238 239 2.773 240 2.765 241 2.764 242 2.772 243 2.769 244 2.771 245 246 247 2.897 248 2.886 249 2.917 250 2.978 251 2.977 252 253 254 3.014 255 3.021 256 257 3.021 258 3.034 259 3.052 260 3.075 261 3.114 262 3.138 263 3.173 264 265 266 3.101 267 3.124 268 3.127 269 3.137 270 3.149 271 3.160 272 3.165 273 3.186 274 3.200 275 276 3.212 277 3.212 278 3.201 279 3.234 280 3.262 281 3.264 282 3.269 283 3.243 284 285 3.249 286 3.284 287 3.301 288 3.286 289 3.290 290 3.332 291 3.344 292 3.323 293 3.281 294 3.295 295 296 3.384 297 3.389 298 3.396 299 3.414 300 301 3.440 302 303 3.435 304 3.458 305 3.484 306 3.520 307 3.526 308 3.542 309 3.543 310 3.549 311 3.568 312 3.567 313 3.597 314 3.574 315 3.583 316 3.596 317 3.589 318 3.576 319 320 3.572 321 3.538 322 3.563 323 3.574 324 3.582 325 3.608 326 3.642 327 3.661 328 3.717 329 3.718 330 3.713 331 3.725 332 3.740 333 3.741 334 3.759 335 3.768 336 3.797 337 3.807 338 3.838 339 3.857 340 3.867 341 3.888 342 3.881 343 3.890 34
Re: [gmx-users] umbrella sample Question
On 8/18/17 10:54 AM, yujie liu wrote: Hello，gromacs user I am a novice, I met some problems when I do this tutorial to learn umbrella sample, at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html. I am using gromacs 5.1.4 and the summary_distances.dat file is not complete while carrying out ‘perl distances.pl’. Some values of distance between COM of Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In fact, I checked out some distxxx.xvg and found which existed a value of distance but why these values can’t write into summary_distances.dat completely by commend ‘perl distances.pl’ ? There is someone met with the situation?? People keep telling me that this happens and no one follows up with a solution. I'd love to solve it once and for all, because I can never reproduce the problem. Run gmx distance yourself, not from the script. Something will fail and you'll get a clear error message that can be used to diagnose the issue. Without that, it's impossible to help. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] umbrella sample Question
Hello，gromacs user I am a novice, I met some problems when I do this tutorial to learn umbrella sample, at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html. I am using gromacs 5.1.4 and the summary_distances.dat file is not complete while carrying out ‘perl distances.pl’. Some values of distance between COM of Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In fact, I checked out some distxxx.xvg and found which existed a value of distance but why these values can’t write into summary_distances.dat completely by commend ‘perl distances.pl’ ? There is someone met with the situation?? Thanks Yours Liu. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
