[gmx-users] Indexing problem when using genconf

Ryan S Davis (rsdavis1) rsdavis1 at memphis.edu
Tue May 31 05:12:15 CEST 2011

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"
  5 [ system ]
  6 CHOL
  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,

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