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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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