Order Parameters calculation for POPC and POPS in multi-component lipid mixture

GROMACS version:2023
GROMACS modification: Yes/No
Here post your question
I have a multi-component lipid mixture in the lipid bilayer and want to calculate the order parameter for POPC and POPS, which are present in the system. However, when I run the command: “gmx order -s step6.2_equilibration.tpr -f step6.2_equilibration.xtc -n sn1.ndx -d z -od deuter_sn1.xvg”. I encounter an error. "Command line:
gmx order -s step6.2_equilibration.tpr -f step6.2_equilibration.xtc -n sn1.ndx -d z -od deuter_sn1.xvg

Taking z axis as normal to the membrane
Reading file step6.2_equilibration.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Using following groups:
Groupname: System First atomname: C1S First atomnr 1
Groupname: Other First atomname: C1S First atomnr 1
Groupname: CER16 First atomname: C1S First atomnr 1
Groupname: BGLC First atomname: C1 First atomnr 104
Groupname: BGAL First atomname: C1 First atomnr 126
Groupname: BGALN First atomname: C1 First atomnr 146
Groupname: ANE5A First atomname: C1 First atomnr 195
Groupname: CHL1 First atomname: C3 First atomnr 1849
Groupname: SSM First atomname: N First atomnr 4809
Groupname: POPE First atomname: N First atomnr 7203
Groupname: POPS First atomname: N First atomnr 13203
Groupname: POPC First atomname: N First atomnr 14473
Groupname: SOD First atomname: SOD First atomnr 24657
Groupname: CLA First atomname: CLA First atomnr 24713
Groupname: TIP3 First atomname: OH2 First atomnr 24751
Groupname: POPS First atomname: N First atomnr 13203

Reading frame 0 time 0.000 Number of elements in first group: 67992
WARNING: distance between atoms 103 and 231 > 0.3 nm (2.711024). Index file might be corrupt.
WARNING: distance between atoms 104 and 232 > 0.3 nm (2.725754). Index file might be corrupt.
WARNING: distance between atoms 105 and 233 > 0.3 nm (2.677751). Index file might be corrupt.
WARNING: distance between atoms 106 and 234 > 0.3 nm (2.652974). Index file might be corrupt.
WARNING: distance between atoms 107 and 235 > 0.3 nm (2.750825). Index file might be corrupt.
WARNING: distance between atoms 108 and 236 > 0.3 nm (2.726624). Index file might be corrupt.
WARNING: distance between atoms 109 and 237 > 0.3 nm (2.780412). Index file might be corrupt.
WARNING: distance between atoms 110 and 238 > 0.3 nm (2.713769). Index file might be corrupt.
WARNING: distance between atoms 111 and 239 > 0.3 nm (2.828425). Index file might be corrupt.
WARNING: distance between atoms 112 and 240 > 0.3 nm (2.894175). Index file might be corrupt.
WARNING: distance between atoms 113 and 241 > 0.3 nm (2.841862). Index file might be corrupt.
WARNING: distance between atoms 114 and 242 > 0.3 nm (3.009158). Index file might be corrupt.
WARNING: distance between atoms 115 and 243 > 0.3 nm (2.828623). Index file might be corrupt.
WARNING: distance between atoms 116 and 244 > 0.3 nm (2.956773). Index file might be corrupt.
WARNING: distance between atoms 117 and 245 > 0.3 nm (2.958525). Index file might be corrupt.
WARNING: distance between atoms 118 and 246 > 0.3 nm (2.949932). Index file might be corrupt.
WARNING: distance between atoms 119 and 247 > 0.3 nm (3.069548). Index file might be corrupt.
WARNING: distance between atoms 120 and 248 > 0.3 nm (3.199051). Index file might be corrupt.
WARNING: distance between atoms 121 and 249 > 0.3 nm (3.100846). Index file might be corrupt.
WARNING: distance between atoms 122 and 250 > 0.3 nm (2.985798). Index file might be corrupt.
WARNING: distance between atoms 123 and 251 > 0.3 nm (3.053642). Index file might be corrupt.
WARNING: distance between atoms 124 and 252 > 0.3 nm (3.336317). Index file might be corrupt.
…" Can you tell me what should I do to resolve this error.

The index files are a bit special for order parameter analysis. Each group in the index file should contain the selection of one kind of atoms in all the molecules you want to analyze. An example for analyzing the sphingoid tail of 90 ceramides in a system:

[ C4S ]
  14  211  408  605  802  999 1196 1393 1590 1787 1984 2181 8890 9010 9130 
9250 9370 9496 9622 9748 9874 10000 10126 10252 10378 10510 10642 10774 10906 11038 
11170 11302 11434 11566 11698 11830 11962 12094 12226 12358 12490 12628 12766 12904 13042 
13180 13318 13456 13594 13732 13870 14008 14146 14284 14422 14560 14698 14836 14974 15112 
15250 15388 15526 15664 15802 15946 16090 16234 16378 16522 16666 16810 16954 17104 17254 
17383 17512 17641 17770 17899 18028 18157 18286 18415 18544 18673 18802 18931 19060 19189 

[ C5S ]
  16  213  410  607  804 1001 1198 1395 1592 1789 1986 2183 8894 9014 9134 
9254 9374 9500 9626 9752 9878 10004 10130 10256 10382 10514 10646 10778 10910 11042 
11174 11306 11438 11570 11702 11834 11966 12098 12230 12362 12494 12632 12770 12908 13046 
13184 13322 13460 13598 13736 13874 14012 14150 14288 14426 14564 14702 14840 14978 15116 
15254 15392 15530 15668 15806 15950 16094 16238 16382 16526 16670 16814 16958 17108 17256 
17385 17514 17643 17772 17901 18030 18159 18288 18417 18546 18675 18804 18933 19062 19191 

[ C6S ]
  18  215  412  609  806 1003 1200 1397 1594 1791 1988 2185 8897 9017 9137 
9257 9377 9503 9629 9755 9881 10007 10133 10259 10385 10517 10649 10781 10913 11045 
11177 11309 11441 11573 11705 11837 11969 12101 12233 12365 12497 12635 12773 12911 13049 
13187 13325 13463 13601 13739 13877 14015 14153 14291 14429 14567 14705 14843 14981 15119 
15257 15395 15533 15671 15809 15953 16097 16241 16385 16529 16673 16817 16961 17111 17258 
17387 17516 17645 17774 17903 18032 18161 18290 18419 18548 18677 18806 18935 19064 19193 

[ C7S ]
  21  218  415  612  809 1006 1203 1400 1597 1794 1991 2188 8900 9020 9140 
9260 9380 9506 9632 9758 9884 10010 10136 10262 10388 10520 10652 10784 10916 11048 
11180 11312 11444 11576 11708 11840 11972 12104 12236 12368 12500 12638 12776 12914 13052 
13190 13328 13466 13604 13742 13880 14018 14156 14294 14432 14570 14708 14846 14984 15122 
15260 15398 15536 15674 15812 15956 16100 16244 16388 16532 16676 16820 16964 17114 17261 
17390 17519 17648 17777 17906 18035 18164 18293 18422 18551 18680 18809 18938 19067 19196 

[ C8S ]
  24  221  418  615  812 1009 1206 1403 1600 1797 1994 2191 8903 9023 9143 
9263 9383 9509 9635 9761 9887 10013 10139 10265 10391 10523 10655 10787 10919 11051 
11183 11315 11447 11579 11711 11843 11975 12107 12239 12371 12503 12641 12779 12917 13055 
13193 13331 13469 13607 13745 13883 14021 14159 14297 14435 14573 14711 14849 14987 15125 
15263 15401 15539 15677 15815 15959 16103 16247 16391 16535 16679 16823 16967 17117 17264 
17393 17522 17651 17780 17909 18038 18167 18296 18425 18554 18683 18812 18941 19070 19199 

[ C9S ]
  27  224  421  618  815 1012 1209 1406 1603 1800 1997 2194 8906 9026 9146 
9266 9386 9512 9638 9764 9890 10016 10142 10268 10394 10526 10658 10790 10922 11054 
11186 11318 11450 11582 11714 11846 11978 12110 12242 12374 12506 12644 12782 12920 13058 
13196 13334 13472 13610 13748 13886 14024 14162 14300 14438 14576 14714 14852 14990 15128 
15266 15404 15542 15680 15818 15962 16106 16250 16394 16538 16682 16826 16970 17120 17267 
17396 17525 17654 17783 17912 18041 18170 18299 18428 18557 18686 18815 18944 19073 19202 

[ C10S ]
  30  227  424  621  818 1015 1212 1409 1606 1803 2000 2197 8909 9029 9149 
9269 9389 9515 9641 9767 9893 10019 10145 10271 10397 10529 10661 10793 10925 11057 
11189 11321 11453 11585 11717 11849 11981 12113 12245 12377 12509 12647 12785 12923 13061 
13199 13337 13475 13613 13751 13889 14027 14165 14303 14441 14579 14717 14855 14993 15131 
15269 15407 15545 15683 15821 15965 16109 16253 16397 16541 16685 16829 16973 17123 17270 
17399 17528 17657 17786 17915 18044 18173 18302 18431 18560 18689 18818 18947 19076 19205 

[ C11S ]
  33  230  427  624  821 1018 1215 1412 1609 1806 2003 2200 8912 9032 9152 
9272 9392 9518 9644 9770 9896 10022 10148 10274 10400 10532 10664 10796 10928 11060 
11192 11324 11456 11588 11720 11852 11984 12116 12248 12380 12512 12650 12788 12926 13064 
13202 13340 13478 13616 13754 13892 14030 14168 14306 14444 14582 14720 14858 14996 15134 
15272 15410 15548 15686 15824 15968 16112 16256 16400 16544 16688 16832 16976 17126 17273 
17402 17531 17660 17789 17918 18047 18176 18305 18434 18563 18692 18821 18950 19079 19208 

[ C12S ]
  36  233  430  627  824 1021 1218 1415 1612 1809 2006 2203 8915 9035 9155 
9275 9395 9521 9647 9773 9899 10025 10151 10277 10403 10535 10667 10799 10931 11063 
11195 11327 11459 11591 11723 11855 11987 12119 12251 12383 12515 12653 12791 12929 13067 
13205 13343 13481 13619 13757 13895 14033 14171 14309 14447 14585 14723 14861 14999 15137 
15275 15413 15551 15689 15827 15971 16115 16259 16403 16547 16691 16835 16979 17129 17276 
17405 17534 17663 17792 17921 18050 18179 18308 18437 18566 18695 18824 18953 19082 19211 

[ C13S ]
  39  236  433  630  827 1024 1221 1418 1615 1812 2009 2206 8918 9038 9158 
9278 9398 9524 9650 9776 9902 10028 10154 10280 10406 10538 10670 10802 10934 11066 
11198 11330 11462 11594 11726 11858 11990 12122 12254 12386 12518 12656 12794 12932 13070 
13208 13346 13484 13622 13760 13898 14036 14174 14312 14450 14588 14726 14864 15002 15140 
15278 15416 15554 15692 15830 15974 16118 16262 16406 16550 16694 16838 16982 17132 17279 
17408 17537 17666 17795 17924 18053 18182 18311 18440 18569 18698 18827 18956 19085 19214 

[ C14S ]
  42  239  436  633  830 1027 1224 1421 1618 1815 2012 2209 8921 9041 9161 
9281 9401 9527 9653 9779 9905 10031 10157 10283 10409 10541 10673 10805 10937 11069 
11201 11333 11465 11597 11729 11861 11993 12125 12257 12389 12521 12659 12797 12935 13073 
13211 13349 13487 13625 13763 13901 14039 14177 14315 14453 14591 14729 14867 15005 15143 
15281 15419 15557 15695 15833 15977 16121 16265 16409 16553 16697 16841 16985 17135 17282 
17411 17540 17669 17798 17927 18056 18185 18314 18443 18572 18701 18830 18959 19088 19217 

[ C15S ]
  45  242  439  636  833 1030 1227 1424 1621 1818 2015 2212 8924 9044 9164 
9284 9404 9530 9656 9782 9908 10034 10160 10286 10412 10544 10676 10808 10940 11072 
11204 11336 11468 11600 11732 11864 11996 12128 12260 12392 12524 12662 12800 12938 13076 
13214 13352 13490 13628 13766 13904 14042 14180 14318 14456 14594 14732 14870 15008 15146 
15284 15422 15560 15698 15836 15980 16124 16268 16412 16556 16700 16844 16988 17138 17285 
17414 17543 17672 17801 17930 18059 18188 18317 18446 18575 18704 18833 18962 19091 19220 

[ C16S ]
  48  245  442  639  836 1033 1230 1427 1624 1821 2018 2215 8927 9047 9167 
9287 9407 9533 9659 9785 9911 10037 10163 10289 10415 10547 10679 10811 10943 11075 
11207 11339 11471 11603 11735 11867 11999 12131 12263 12395 12527 12665 12803 12941 13079 
13217 13355 13493 13631 13769 13907 14045 14183 14321 14459 14597 14735 14873 15011 15149 
15287 15425 15563 15701 15839 15983 16127 16271 16415 16559 16703 16847 16991 17141 17288 
17417 17546 17675 17804 17933 18062 18191 18320 18449 18578 18707 18836 18965 19094 19223 

[ C17S ]
  51  248  445  642  839 1036 1233 1430 1627 1824 2021 2218 8930 9050 9170 
9290 9410 9536 9662 9788 9914 10040 10166 10292 10418 10550 10682 10814 10946 11078 
11210 11342 11474 11606 11738 11870 12002 12134 12266 12398 12530 12668 12806 12944 13082 
13220 13358 13496 13634 13772 13910 14048 14186 14324 14462 14600 14738 14876 15014 15152 
15290 15428 15566 15704 15842 15986 16130 16274 16418 16562 16706 16850 16994 17144 17291 
17420 17549 17678 17807 17936 18065 18194 18323 18452 18581 18710 18839 18968 19097 19226 

[ C18S ]
  54  251  448  645  842 1039 1236 1433 1630 1827 2024 2221 8933 9053 9173 
9293 9413 9539 9665 9791 9917 10043 10169 10295 10421 10553 10685 10817 10949 11081 
11213 11345 11477 11609 11741 11873 12005 12137 12269 12401 12533 12671 12809 12947 13085 
13223 13361 13499 13637 13775 13913 14051 14189 14327 14465 14603 14741 14879 15017 15155 
15293 15431 15569 15707 15845 15989 16133 16277 16421 16565 16709 16853 16997 17147 17294 
17423 17552 17681 17810 17939 18068 18197 18326 18455 18584 18713 18842 18971 19100 19229 

I gave the command “gmx make_ndx -f step6.2_equilibration.tpr -o sn1.ndx” and select POPS where I have [ POPS ]

13203 13204 13205 13206 13207 13208 13209 13210 13211 13212 13213 13214 13215 13216 13217

13218 13219 13220 13221 13222 13223 13224 13225 13226 13227 13228 13229 13230 13231 13232

13233 13234 13235 13236 13237 13238 13239 13240 13241 13242 13243 13244 13245 13246 13247

13248 13249 13250 13251 13252 13253 13254 13255 13256 13257 13258 13259 13260 13261 13262

13263 13264 13265 13266 13267 13268 13269 13270 13271 13272 13273 13274 13275 13276 13277

13278 13279 13280 13281 13282 13283 13284 13285 13286 13287 13288 13289 13290 13291 13292

13293 13294 13295 13296 13297 13298 13299 13300 13301 13302 13303 13304 13305 13306 13307

13308 13309 13310 13311 13312 13313 13314 13315 13316 13317 13318 13319 13320 13321 13322

13323 13324 13325 13326 13327 13328 13329 13330 13331 13332 13333 13334 13335 13336 13337

13338 13339 13340 13341 13342 13343 13344 13345 13346 13347 13348 13349 13350 13351 13352

13353 13354 13355 13356 13357 13358 13359 13360 13361 13362 13363 13364 13365 13366 13367

13368 13369 13370 13371 13372 13373 13374 13375 13376 13377 13378 13379 13380 13381 13382

13383 13384 13385 13386 13387 13388 13389 13390 13391 13392 13393 13394 13395 13396 13397

13398 13399 13400 13401 13402 13403 13404 13405 13406 13407 13408 13409 13410 13411 13412

13413 13414 13415 13416 13417 13418 13419 13420 13421 13422 13423 13424 13425 13426 13427

13428 13429 13430 13431 13432 13433 13434 13435 13436 13437 13438 13439 13440 13441 13442

13443 13444 13445 13446 13447 13448 13449 13450 13451 13452 13453 13454 13455 13456 13457

13458 13459 13460 13461 13462 13463 13464 13465 13466 13467 13468 13469 13470 13471 13472

13473 13474 13475 13476 13477 13478 13479 13480 13481 13482 13483 13484 13485 13486 13487

13488 13489 13490 13491 13492 13493 13494 13495 13496 13497 13498 13499 13500 13501 13502

13503 13504 13505 13506 13507 13508 13509 13510 13511 13512 13513 13514 13515 13516 13517

13518 13519 13520 13521 13522 13523 13524 13525 13526 13527 13528 13529 13530 13531 13532

13533 13534 13535 13536 13537 13538 13539 13540 13541 13542 13543 13544 13545 13546 13547

13548 13549 13550 13551 13552 13553 13554 13555 13556 13557 13558 13559 13560 13561 13562

13563 13564 13565 13566 13567 13568 13569 13570 13571 13572 13573 13574 13575 13576 13577

13578 13579 13580 13581 13582 13583 13584 13585 13586 13587 13588 13589 13590 13591 13592

13593 13594 13595 13596 13597 13598 13599 13600 13601 13602 13603 13604 13605 13606 13607

13608 13609 13610 13611 13612 13613 13614 13615 13616 13617 13618 13619 13620 13621 13622

13623 13624 13625 13626 13627 13628 13629 13630 13631 13632 13633 13634 13635 13636 13637

13638 13639 13640 13641 13642 13643 13644 13645 13646 13647 13648 13649 13650 13651 13652

13653 13654 13655 13656 13657 13658 13659 13660 13661 13662 13663 13664 13665 13666 13667

13668 13669 13670 13671 13672 13673 13674 13675 13676 13677 13678 13679 13680 13681 13682

13683 13684 13685 13686 13687 13688 13689 13690 13691 13692 13693 13694 13695 13696 13697

13698 13699 13700 13701 13702 13703 13704 13705 13706 13707 13708 13709 13710 13711 13712

13713 13714 13715 13716 13717 13718 13719 13720 13721 13722 13723 13724 13725 13726 13727

13728 13729 13730 13731 13732 13733 13734 13735 13736 13737 13738 13739 13740 13741 13742

13743 13744 13745 13746 13747 13748 13749 13750 13751 13752 13753 13754 13755 13756 13757

13758 13759 13760 13761 13762 13763 13764 13765 13766 13767 13768 13769 13770 13771 13772

13773 13774 13775 13776 13777 13778 13779 13780 13781 13782 13783 13784 13785 13786 13787

13788 13789 13790 13791 13792 13793 13794 13795 13796 13797 13798 13799 13800 13801 13802

13803 13804 13805 13806 13807 13808 13809 13810 13811 13812 13813 13814 13815 13816 13817

13818 13819 13820 13821 13822 13823 13824 13825 13826 13827 13828 13829 13830 13831 13832

13833 13834 13835 13836 13837 13838 13839 13840 13841 13842 13843 13844 13845 13846 13847

13848 13849 13850 13851 13852 13853 13854 13855 13856 13857 13858 13859 13860 13861 13862

13863 13864 13865 13866 13867 13868 13869 13870 13871 13872 13873 13874 13875 13876 13877

13878 13879 13880 13881 13882 13883 13884 13885 13886 13887 13888 13889 13890 13891 13892

13893 13894 13895 13896 13897 13898 13899 13900 13901 13902 13903 13904 13905 13906 13907

13908 13909 13910 13911 13912 13913 13914 13915 13916 13917 13918 13919 13920 13921 13922

13923 13924 13925 13926 13927 13928 13929 13930 13931 13932 13933 13934 13935 13936 13937

13938 13939 13940 13941 13942 13943 13944 13945 13946 13947 13948 13949 13950 13951 13952

13953 13954 13955 13956 13957 13958 13959 13960 13961 13962 13963 13964 13965 13966 13967

13968 13969 13970 13971 13972 13973 13974 13975 13976 13977 13978 13979 13980 13981 13982

13983 13984 13985 13986 13987 13988 13989 13990 13991 13992 13993 13994 13995 13996 13997

13998 13999 14000 14001 14002 14003 14004 14005 14006 14007 14008 14009 14010 14011 14012

14013 14014 14015 14016 14017 14018 14019 14020 14021 14022 14023 14024 14025 14026 14027

14028 14029 14030 14031 14032 14033 14034 14035 14036 14037 14038 14039 14040 14041 14042

14043 14044 14045 14046 14047 14048 14049 14050 14051 14052 14053 14054 14055 14056 14057

14058 14059 14060 14061 14062 14063 14064 14065 14066 14067 14068 14069 14070 14071 14072

14073 14074 14075 14076 14077 14078 14079 14080 14081 14082 14083 14084 14085 14086 14087

14088 14089 14090 14091 14092 14093 14094 14095 14096 14097 14098 14099 14100 14101 14102

14103 14104 14105 14106 14107 14108 14109 14110 14111 14112 14113 14114 14115 14116 14117

14118 14119 14120 14121 14122 14123 14124 14125 14126 14127 14128 14129 14130 14131 14132

14133 14134 14135 14136 14137 14138 14139 14140 14141 14142 14143 14144 14145 14146 14147

14148 14149 14150 14151 14152 14153 14154 14155 14156 14157 14158 14159 14160 14161 14162

14163 14164 14165 14166 14167 14168 14169 14170 14171 14172 14173 14174 14175 14176 14177

14178 14179 14180 14181 14182 14183 14184 14185 14186 14187 14188 14189 14190 14191 14192

14193 14194 14195 14196 14197 14198 14199 14200 14201 14202 14203 14204 14205 14206 14207

14208 14209 14210 14211 14212 14213 14214 14215 14216 14217 14218 14219 14220 14221 14222

14223 14224 14225 14226 14227 14228 14229 14230 14231 14232 14233 14234 14235 14236 14237

14238 14239 14240 14241 14242 14243 14244 14245 14246 14247 14248 14249 14250 14251 14252

14253 14254 14255 14256 14257 14258 14259 14260 14261 14262 14263 14264 14265 14266 14267

14268 14269 14270 14271 14272 14273 14274 14275 14276 14277 14278 14279 14280 14281 14282

14283 14284 14285 14286 14287 14288 14289 14290 14291 14292 14293 14294 14295 14296 14297

14298 14299 14300 14301 14302 14303 14304 14305 14306 14307 14308 14309 14310 14311 14312

14313 14314 14315 14316 14317 14318 14319 14320 14321 14322 14323 14324 14325 14326 14327

14328 14329 14330 14331 14332 14333 14334 14335 14336 14337 14338 14339 14340 14341 14342

14343 14344 14345 14346 14347 14348 14349 14350 14351 14352 14353 14354 14355 14356 14357

14358 14359 14360 14361 14362 14363 14364 14365 14366 14367 14368 14369 14370 14371 14372

14373 14374 14375 14376 14377 14378 14379 14380 14381 14382 14383 14384 14385 14386 14387

14388 14389 14390 14391 14392 14393 14394 14395 14396 14397 14398 14399 14400 14401 14402

14403 14404 14405 14406 14407 14408 14409 14410 14411 14412 14413 14414 14415 14416 14417

14418 14419 14420 14421 14422 14423 14424 14425 14426 14427 14428 14429 14430 14431 14432

14433 14434 14435 14436 14437 14438 14439 14440 14441 14442 14443 14444 14445 14446 14447

14448 14449 14450 14451 14452 14453 14454 14455 14456 14457 14458 14459 14460 14461 14462

14463 14464 14465 14466 14467 14468 14469 14470 14471 14472

and after that I give “gmx order -s step6.2_equilibration.tpr -f step6.2_equilibration.xtc -n sn1.ndx -d z -od deuter_sn1.xvg” command but deuter_sn1.xvg file is empty.