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

[David van der Spoel]

Alan Dodd wrote:
> 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?

please submit a bugzilla with complete input.

> 
> 
> 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
> q
> +
> /home/ad0303/GROMACS4/bin/g_order -s $tpr -f trjShort -o test -n testyleaf2 -nice 0 -szonly
> 
> result:
> 
> 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
> 
> sk-dist.xvg
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se