[gmx-users] index file for g_order

[Alan Dodd]

The first and last carbons are not calculated. 
GROMACS needs to use a C-C bond on either side of each
carbon to place the hydrogens, and hence calculate the
order parameter.

--- Arneh Babakhani <ababakha at mccammon.ucsd.edu>
wrote:

> Hello,
> 
> 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?
> 
> Thanks,
> 
> Arneh
> 
> -----------------------------------
> 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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