Dear GROMACS community,
I am new to the (virtual) neighborhood (but not to the use of MD simulations)!
I tried to use gmx minddist, but received a segmentation fault error. My command-line input was:
gmx mindist -n index.ndx -f prep.xtc
The groups I selected from index.ndx file are below. Each group consists of 77 atoms.
[ igr1 ]
4397 4421 4453 4480 4515 4544 4571 4593 4617 4655 4689 4721 4758 4783 4804 4842 4882 4900 4941 4967 4996 5022 5047 5084 5117 5152 5171 5199 5216 5240 5261 5282 5319 5347 5377 5423 5448 5469 5503 5533 5574 5597 5628 5649 5679 5701 5735 5758 5780 5807 5848 5871 5906 5936 5954 5984 6014 6040 6078 6113 6146 6183 6205 6236 6265 6279 6308 6334 6370 6391 6415 6433 6476 6496 6519 6545 6574
[ igr2 ]
9 33 65 92 127 156 183 205 229 267 301 333 370 395 416 454 494 512 553 579 608 634 659 696 729 764 783 811 828 852 873 894 931 959 989 1035 1060 1081 1115 1145 1186 1209 1240 1261 1291 1313 1347 1370 1392 1419 1453 1476 1511 1541 1559 1589 1619 1645 1683 1718 1751 1788 1810 1841 1870 1884 1913 1939 1975 1996 2020 2038 2081 2101 2124 2150 2179
The segmentation fault occurred on frame 200 out of 400. I have also received segmentation faults for groups of larger atoms after fewer frames were processed.
I’m using version 2022.3.
Please let me know how I can resolved this issue? Should I simply reduce my selections to analyze more frames?
If you need any other information to be helpful, please just let me know.
Best,
Matthew J. Guberman-Pfeffer