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

[Justin A. Lemkul]

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
file).

-Justin

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.



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

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