Gromacs
Register

g order

    The g_order program calculates order parameters for carbon atoms along an acyl chain, most often a membrane lipid. A common mistake that users make is preparing the index file incorrectly. The index file must specify the carbon atoms of a single acyl chain (sn-1 or sn-2). For example, if you are analyzing DPPC from Tieleman's site:

    make_ndx -f dppc128.pdb -o sn1.ndx
> a C34
> a C36
> ...
> a C50
> del 0-5
> q

    In the above example, the individual types of carbon atoms along the sn-1 chain are specified, and the default index groups in the index file (System, Other, DPP, Water, SOL, non-Water) are deleted.

     

    Notes on Output

    The output of g_order is numbered incorrectly for all GROMACS versions up to, and including, 4.5.4.  Deuterium order parameters are calculated only for carbons 2 to n-1 of the lipid chain (assuming the carbonyl carbon is atom 1 and the whole chain is being analyzed).  In the case of most phospholipids, this means that the carbonyl and terminal methyl carbons are not included in the output (which makes sense, given the nature of the calculation).  Despite this fact, the atom numbering in deuter.xvg begins with 1.  Thus, proper interpretation of the output requires re-numbering to start from carbon 2.  In the case of DPPC, the output files for the sn-1 and sn-2 chains will be numbered 1-14.  There are 16 carbon atoms in the acyl chains, for which only 14 order parameters can be calculated, but these values correspond, in reality, to carbons 2-15.

     

    Calculating Order Parameters for Unsaturated Carbons

    The g_order help description indicates that the -unsat option cannot be combined with normal order parameter calculations, due to the fact that different geometric parameters must be calculated for sp2 and sp3 carbons.  Thus, to obtain order parameters for unsaturated carbons, two iterations of g_order are required.  The first will calculate order parameters for all carbons in the chain using normal options.  The second should be conducted on an index file containing only Cn-1, Cn, Cn+1, and Cn+2, wherein Cn and Cn+1 are the carbon atoms connected by the double bond.  Invoke g_order with the -unsat option and replace the resulting order parameter values for Cn and Cn+1 in the original output files with those obtained in this second calculation.

     

    Reference

    Attach file

    Files0

     
    Page last modified 20:27, 19 May 2011 by JLemkul?