I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and everything seemed to work fine exept that annoying feature that the command does not reorder the molecule types, so I end up with a .top file looking like this...
1 #include "martini_v2.1.itp" 2 #include "martini_v2.0_lipids.itp" 3 #include "martini_v2.0_cholesterol.itp" 4 5 [ system ] 6 CHOL 7 8 [ molecules ] 9 DPPC 832 10 CHOL 208 11 W 8320 12 DPPC 832 13 CHOL 208 14 W 8320 15 DPPC 832 16 CHOL 208 17 W 8320 18 DPPC 832 19 CHOL 208 20 W 8320 Anyway, I run the simulation...no errors. I make an ndx file using make_ndx...indices look fine despite the repetitive order. HOWEVER, when I try to run commands such as trjconv with the index file as input, it reads all the way up to the first block of Waters and quits with the error """ Program trjconv, VERSION 4.0.7 Source code file: gmx_trjconv.c, line: 1037 Fatal error: Index[29952] 46593 is larger than the number of atoms in the trajectory file (46592) """ which I didnt expect, but makes perfect sense knowing that I specified in the .mdp file to not output water to the xtc file... """ xtc-grps = dppc chol """ Normally this isnt an issue because waters are typically last in the topology. But, I still need access to this data. How can I force the post-processing commands to read past the absent water blocks? The only options I see at the moments is to 1) scrap genconf, make new topology somehow, and rerun 2) reset to output water, and rerun 3) limit my analysis to the very sparse output from the .trr file Thanks for any suggestions, Ryan-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
