[gmx-users] g_mindist clarification

Fri Jan 28 13:08:13 CET 2011

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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