Justin A. Lemkul wrote: > > > Ryan S Davis (rsdavis1) wrote: >> 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 >> > > I see two viable options, one of which is to use your option 1 via a few > standard Unix tools to create a proper coordinate file, i.e.: > > grep DPPC conf.gro > dppc > grep CHOL conf.gro > chol > grep W conf.gro > w > > cat dppc chol w > system.gro > > Add a title, number of atoms, and box vectors at the end, and you're > done. Then sum up the entries in [molecules] and the system should run > just fine. > > The second option is to just create a dummy system that has only DPPC > and CHOL molecules. Take your input coordinate file, strip out the > waters, and renumber with genconf. Remove all W blocks from the .top > and create a new .tpr file. This should now match the number of atoms in > the trajectory and the order in which they appear. >
...or just do this all in one step with tpbconv. I always manage to quickly think of the hardest way to do things :) -Justin Thanks, got it working with tpbconv. It would be nice to have an option on genconf to reorder the molecule types in the output... Not that I am willing to make that modification myself, ha :) Ryan-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
