[gmx-users] index file for g_order

[Arneh Babakhani]

Hi Alan, great, thanks, I suspected something like that.

Then, is there a way to calculate the Scd order parameters for these 
carbons, given that there are no explicit hydrogens???

Arneh

Alan Dodd wrote:
> 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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>
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