[gmx-users] Re:Re: g_order in GROMACS 3.3.2 and 3.3.1

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 7 17:06:10 CEST 2007

Each atom type must be in a separate group.  For example:

> a C17
> a C18

(and so forth for the rest of the carbon atoms in the chain)

The rest of your process is fine (deleting out the other groups from the index


Quoting ªL´­µ½ <d93543002 at ntu.edu.tw>:

> Dear all GROMACS user :
>     After generating the .ndx file which contained only one group that one
> tail of DPPC,
>     I use g_order to calculate order parameters. But there are nothing in
> deuter.xvg and order.xvg file.
>     The process is listed below:
>     step1: make_ndx -f XXX.pdb -o index.ndx
>              then type : a C17 C18 ... C31     (C31 is methyl and C17...C30
> is methylene in one tail of DPPC lipid)
>              then type : name 3 sn_1        (0 is for system, 1 is for DPPC,
> 2 is for SOL )
>              then type : q
>     step2 : delete all groups in the index.ndx except sn_1 group.
>     step3 : g_order -f YYY.pdb -n index.ndx -s .tpr -od
>      Can someone tell me what wrong is in my process ?
>          Thank you very much.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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