[gmx-users] g_order atom distance warning

[Stephen M. Dutz]

Hello,
Over the last day I've been working with the g_order utility, assessing the order parameters of a protein embedded POPC system.  I created an index file for one of the carbon chains of the POPC, it looks as follows:

[ POPC_&_C34 ]
 342  394  446  498  550  602  654  706  758  810  862  914  966 1018 1070
1122 1174 1226 1278 1330 1382 1434 1486 1538 1590 1642 1694 1746 1798 1850
1902 1954 2006 2058 2110 2162 2214 2266 2318 2370 2422 2474 2526 2578 2630
2682 2734 2786 2838 2890 2942 2994 3046 3098 3150 3202 3254 3306 3358 3410
3462 3514 3566 3618 3670 3722 3774 3826 3878 3930 3982 4034 4086 4138 4190
4242 4294 4346 4398 4450 4502 4554 4606 4658 4710 4762 4814 4866 4918 4970
5022 5074 5126 5178 5230 5282
[ POPC_&_C36 ]
 344  396  448  500  552  604  656  708  760  812  864  916  968 1020 1072
1124 1176 1228 1280 1332 1384 1436 1488 1540 1592 1644 1696 1748 1800 1852
1904 1956 2008 2060 2112 2164 2216 2268 2320 2372 2424 2476 2528 2580 2632
2684 2736 2788 2840 2892 2944 2996 3048 3100 3152 3204 3256 3308 3360 3412
3464 3516 3568 3620 3672 3724 3776 3828 3880 3932 3984 4036 4088 4140 4192
4244 4296 4348 4400 4452 4504 4556 4608 4660 4712 4764 4816 4868 4920 4972
5024 5076 5128 5180 5232 5284
[ POPC_&_C37 ]
 345  397  449  501  553  605  657  709  761  813  865  917  969 1021 1073
1125 1177 1229 1281 1333 1385 1437 1489 1541 1593 1645 1697 1749 1801 1853
1905 1957 2009 2061 2113 2165 2217 2269 2321 2373 2425 2477 2529 2581 2633
2685 2737 2789 2841 2893 2945 2997 3049 3101 3153 3205 3257 3309 3361 3413
3465 3517 3569 3621 3673 3725 3777 3829 3881 3933 3985 4037 4089 4141 4193
4245 4297 4349 4401 4453 4505 4557 4609 4661 4713 4765 4817 4869 4921 4973
5025 5077 5129 5181 5233 5285
[ POPC_&_C38 ]
 346  398  450  502  554  606  658  710  762  814  866  918  970 1022 1074
1126 1178 1230 1282 1334 1386 1438 1490 1542 1594 1646 1698 1750 1802 1854
etc.

Thus the atoms are categorized by their position in the POPC carbon chain.  I then run the following command:

g_order_mpi -f traj.trr -n index.ndx -s topol.tpr -o order.xvg -od deuter.xvg

The program runs, but continuously spits out this warning (with different atom numbers and distances):

WARNING: distance between atoms 5243 and 5245 > 0.3 nm (6.320851). Index file might be corrupt.

The atom numbers are usually two apart, as seen here.  I've searched the mail list for this warning however found nothing.  If anyone has experienced this problem I would greatly appreciate some insight.  When I start at a time that is farther into the simulation I usually don't observe this error, however it will occasionally still pop up.

Thank you in advance,
Steve

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"Mediocrity breeds insecurity and paranoia."
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