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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
