Gromacs

g order

    Table of contents
    1. 1. Reference

    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 0-2
    > 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, DPPC, SOL) are deleted.

     

    Reference

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