Chandan Choudhury wrote:
Hi all !!
Can some one clarify me what the g_mindist does. As far as I understood,
it takes two inputs from the index file. If I have more than one entry
in both of the indexes than how would g_mindist function?
g_mindist finds the minimum distance between any two atom pairs in the supplied
group(s).
-Justin
eg; echo "7 8" | g_mindist -s ../md30-60.tpr -n index.ndx -f
../30-60.part0004.trr -od mindist.xvg -nice 0 -b 35000 -e 40000 -xvgr
My 7th and 8th indexes are :
[ N ]
1 11 20 29 38 47 56 65 74 83 92 101 110 119
128 137 146 155
164 173 183 193 202 211 220 229 238 247 256 265 274 283
292 301 310 319
328 337 346 355 365 375 384 393 402 411 420 429 438 447
456 465 474 483
492 501 510 519 528 537 547 557 566 575 584 593 602 611
620 629 638 647
656 665 674 683 692 701 710 719 729 739 748 757 766 775
784 793 802 811
820 829 838 847 856 865 874 883 892 901 911 921 930 939
948 957 966 975
984 993 1002 1011 1020 1029 1038 1047 1056 1065 1074 1083 1093 1103
1112 1121 1130 1139
1148 1157 1166 1175 1184 1193 1202 1211 1220 1229 1238 1247 1256 1265
1275 1285 1294 1303
1312 1321 1330 1339 1348 1357 1366 1375 1384 1393 1402 1411 1420 1429
1438 1447 1457 1467
1476 1485 1494 1503 1512 1521 1530 1539 1548 1557 1566 1575 1584 1593
1602 1611 1620 1629
1639 1649 1658 1667 1676 1685 1694 1703 1712 1721 1730 1739 1748 1757
1766 1775 1784 1793
1802 1811
[ O ]
1858 1960 2062 2164 2266 2368 2470 2572 2674 2776 2878 2980 3082 3184
3286 3388 3490 3592
3694 3796 3898 4000 4102 4204 4306 4408 4510 4612 4714 4816 4918 5020
5122 5224 5326 5428
5530 5632 5734 5836 5938 6040 6142 6244 6346 6448 6550 6652 6754 1865
1967 2069 2171 2273
2375 2477 2579 2681 2783 2885 2987 3089 3191 3293 3395 3497 3599 3701
3803 3905 4007 4109
4211 4313 4415 4517 4619 4721 4823 4925 5027 5129 5231 5333 5435 5537
5639 5741 5843 5945
6047 6149 6251 6353 6455 6557 6659 6761 1872 1974 2076 2178 2280 2382
2484 2586 2688 2790
2892 2994 3096 3198 3300 3402 3504 3606 3708 3810 3912 4014 4116 4218
4320 4422 4524 4626
4728 4830 4932 5034 5136 5238 5340 5442 5544 5646 5748 5850 5952 6054
6156 6258 6360 6462
6564 6666 6768 1879 1981 2083 2185 2287 2389 2491 2593 2695 2797 2899
3001 3103 3205 3307
3409 3511 3613 3715 3817 3919 4021 4123 4225 4327 4429 4531 4633 4735
4837 4939 5041 5143
5245 5347 5449 5551 5653 5755 5857 5959 6061 6163 6265 6367 6469 6571
6673 6775 1886 1988
2090 2192 2294 2396 2498 2600 2702 2804 2906 3008 3110 3212 3314 3416
3518 3620 3722 3824
3926 4028 4130 4232 4334 4436 4538 4640 4742 4844 4946 5048 5150 5252
5354 5456 5558 5660
5762 5864 5966 6068 6170 6272 6374 6476 6578 6680 6782 1893 1995 2097
2199 2301 2403 2505
2607 2709 2811 2913 3015 3117 3219 3321 3423 3525 3627 3729 3831 3933
4035 4137 4239 4341
4443 4545 4647 4749 4851 4953 5055 5157 5259 5361 5463 5565 5667 5769
5871 5973 6075 6177
6279 6381 6483 6585 6687 6789 1900 2002 2104 2206 2308 2410 2512 2614
2716 2818 2920 3022
3124 3226 3328 3430 3532 3634 3736 3838 3940 4042 4144 4246 4348 4450
4552 4654 4756 4858
4960 5062 5164 5266 5368 5470 5572 5674 5776 5878 5980 6082 6184 6286
6388 6490 6592 6694
6796 1907 2009 2111 2213 2315 2417 2519 2621 2723 2825 2927 3029 3131
3233 3335 3437 3539
3641 3743 3845 3947 4049 4151 4253 4355 4457 4559 4661 4763 4865 4967
5069 5171 5273 5375
5477 5579 5681 5783 5885 5987 6089 6191 6293 6395 6497 6599 6701 6803
1914 2016 2118 2220
2322 2424 2526 2628 2730 2832 2934 3036 3138 3240 3342 3444 3546 3648
3750 3852 3954 4056
4158 4260 4362 4464 4566 4668 4770 4872 4974 5076 5178 5280 5382 5484
5586 5688 5790 5892
5994 6096 6198 6300 6402 6504 6606 6708 6810 1921 2023 2125 2227 2329
2431 2533 2635 2737
2839 2941 3043 3145 3247 3349 3451 3553 3655 3757 3859 3961 4063 4165
4267 4369 4471 4573
4675 4777 4879 4981 5083 5185 5287 5389 5491 5593 5695 5797 5899 6001
6103 6205 6307 6409
6511 6613 6715 6817
With one entry in the g_mindist (-od) and g_dist produces the same graph.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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