[gmx-users] Re: Indexing problem when using genconf

[Mark Abraham]

On 4/06/2011 2:52 PM, Ryan S Davis (rsdavis1) wrote:
> 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

Sorry, I didn't see this discussion first time around. tpbconv allows 
you to create a "subset" .tpr for this kind of purpose. This makes 1) easy.

Mark