[gmx-users] g_order post - 3.3.1 (yes, again).

Alan Dodd anoddlad at yahoo.com
Sat Nov 29 13:00:11 CET 2008

Hello all,
I've been having a nightmare of a time trying to get order parameters for my lipids.  All pre-3.3 files I have can be processed quite happily with a version of g_order from 3.2.1, but I can't seem to get 4.0 (or 3.3.1) to produce the basic order.xvg.  I've tried specifying all carbons to be calculated in a single group - order.xvg never gets produced.  Specifying each equivalent atom in a different group, as worked for 3.2.1, doesn't work either - it only asks for one group, and even if you specify one group to just give it one type of carbon, that still doesn't produce order.xvg.  I get sg-ang and sk-dist (although sg-ang is a long sequence of zeroes at each timepoint), so the program is working, just not giving out the result I want at the end.  Does anyone have an idea what I'm doing wrong, or alternatively have a protocol that they know works for them?

Technical stuff for the approach I use that I think SHOULD work (have tried several other variations):

Commands I run (leaflet.ndx contains atoms from one leaflet in group 0, other leaflet in group 1):

make_ndx -f $tpr -n leaflet -o testyleaf2 <<+
t LP2 | t LP3 | t LC | a C24 | a C25 | a C45 | a C46
1 & 2
del 0
del 0
del 0
/home/ad0303/GROMACS4/bin/g_order -s $tpr -f trjShort -o test -n testyleaf2 -nice 0 -szonly


Reading file topol1.tpr, VERSION 3.2.1 (single precision)
Reading file topol1.tpr, VERSION 3.2.1 (single precision)
Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:
Group     0 (leaflet2_&_LP2_LP3_LC_C24_C25_C45_C46) has  2304 elements
There is one group in the index
Reading frame       0 time    0.000
Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.3#
Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.3#
Reading frame      60 time   45.750
gcq#151: "I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart)

files output:  sg-ang.xvg, sk-dist.xvg

sg-ang.xvg (small excerpt):
0.000000 0.000000
0.750000 0.000000
1.500000 0.000000
2.250000 0.000000
3.000000 0.000000
3.750000 0.000000
4.500000 0.000000
5.250000 0.000000
6.750000 0.000000
7.500000 0.000000

0.000000 0.025605
0.750000 0.025660
1.500000 0.025662
2.250000 0.025649
3.000000 0.025555
3.750000 0.025473
4.500000 0.025505
5.250000 0.025541


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