[gmx-users] index file for g_order

Arneh Babakhani ababakha at mccammon.ucsd.edu
Mon Jun 5 18:47:50 CEST 2006


Now with the g_order bug fixed (see bugzilla #84) , I'm trying to 
calculate the orderparameters for 13 carbon atoms of the the sn2 chain 
(carbons 2B thru 2N) of a DMPC membrane.   So I create an index file, 
make a group for each type of carbon, then run g_order.

The groups in the index file are recognized (as can be seen below, where 
I've pasted an excerpt from my terminal).  All 13 carbon groups are there. 

But the output is a list of order parameters for only 11 carbons (I 
think the last two groups, C2M and C2N, are truncated off).   Is this 
right? If so, how do I calculate the order parameters for C2M and C2N ?  
Or, is this another bug?



Taking z axis as normal to the membrane
Reading file ../FullMD1.tpr, VERSION 3.1.4 (single precision)
Note: tpx file_version 24, software version 40
Note: nLincsIter not in run input file, setting it to 1
Using following groups:
Groupname: C2B First atomname: C2B First atomnr 16
Groupname: C2C First atomname: C2C First atomnr 17
Groupname: C2D First atomname: C2D First atomnr 18
Groupname: C2E First atomname: C2E First atomnr 19
Groupname: C2F First atomname: C2F First atomnr 20
Groupname: C2G First atomname: C2G First atomnr 21
Groupname: C2H First atomname: C2H First atomnr 22
Groupname: C2I First atomname: C2I First atomnr 23
Groupname: C2J First atomname: C2J First atomnr 24
Groupname: C2K First atomname: C2K First atomnr 25
Groupname: C2L First atomname: C2L First atomnr 26
Groupname: C2M First atomname: C2M First atomnr 27
Groupname: C2N First atomname: C2N First atomnr 28

trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000   Number of elements in first group: 128
Last frame        150 time  150.000

Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.225996 , y=-0.226754, z=0.452751
Atom 2 Tensor: x=-0.22165 , y=-0.246523, z=0.468173
Atom 3 Tensor: x=-0.229328 , y=-0.215539, z=0.444867
Atom 4 Tensor: x=-0.230127 , y=-0.199614, z=0.429741
Atom 5 Tensor: x=-0.24599 , y=-0.185492, z=0.431482
Atom 6 Tensor: x=-0.221037 , y=-0.179952, z=0.400989
Atom 7 Tensor: x=-0.226934 , y=-0.170633, z=0.397566
Atom 8 Tensor: x=-0.203112 , y=-0.165726, z=0.368838
Atom 9 Tensor: x=-0.191929 , y=-0.145227, z=0.337156
Atom 10 Tensor: x=-0.164109 , y=-0.118401, z=0.28251
Atom 11 Tensor: x=-0.154092 , y=-0.0753129, z=0.229405

Back Off! I just backed up order.xvg to ./#order.xvg.11#

Back Off! I just backed up deuter.xvg to ./#deuter.xvg.7#

gcq#146: "We All Get the Flu, We All Get Aids" (LIVE)

[ababakha at chelinuxtest OrderParameters]$

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