[gmx-users] problem in g_order

[Erik Marklund]

I see one typo. See below.

Bing Bing skrev:
> Dear all,
> I had created 3-21 group of sn1 chain for order analysis. I have issued:-
>
> make_ndx_d -f md_0_1.tpr -o sn1.dx
Here's the typo. You probably have an index file named sn1.dx.ndx
>
> > a C15
>
> Found 128 atoms with name C15
>
>   3 C15                 :   128 atoms
>
> > a C16
>
> Found 0 atoms with name C16
> Group is empty
>
> > a C17
>
> Found 128 atoms with name C17
>
>   4 C17                 :   128 atoms
>
> > a C18
>
> Found 128 atoms with name C18
>
>   5 C18                 :   128 atoms
>
> > a C19
>
> Found 128 atoms with name C19
>
>   6 C19                 :   128 atoms
>
> > a C20
>
> Found 128 atoms with name C20
>
>   7 C20                 :   128 atoms
>
> > a C21
>
> Found 128 atoms with name C21
>
>   8 C21                 :   128 atoms
>
> > a C22
>
> Found 128 atoms with name C22
>
>   9 C22                 :   128 atoms
>
> > a C23
>
> Found 128 atoms with name C23
>
>  10 C23                 :   128 atoms
>
> > a C24
>
> Found 128 atoms with name C24
>
>  11 C24                 :   128 atoms
>
> > a C25
>
> Found 128 atoms with name C25
>
>  12 C25                 :   128 atoms
>
> > a C26
>
> Found 128 atoms with name C26
>
>  13 C26                 :   128 atoms
>
> > a C27
>
> Found 128 atoms with name C27
>
>  14 C27                 :   128 atoms
>
> > a C28
>
> Found 128 atoms with name C28
>
>  15 C28                 :   128 atoms
>
> > a C29
>
> Found 128 atoms with name C29
>
>  16 C29                 :   128 atoms
>
> > a C30
>
> Found 128 atoms with name C30
>
>  17 C30                 :   128 atoms
>
> > a C30
>
> Found 128 atoms with name C30
>
>  18 C30                 :   128 atoms
>
> > a C31
>
> Found 128 atoms with name C31
>
>  19 C31                 :   128 atoms
>
> > a CA1
>
> Found 128 atoms with name CA1
>
>  20 CA1                 :   128 atoms
>
> > a CA2
>
> Found 128 atoms with name CA2
>
>  21 CA2                 :   128 atoms
>
> >del 0-2
>
> Removed group 0 'System'
> Removed group 1 'POPC'
> Removed group 2 'SOL'
>
> Subsequently, i did this:-
>
> g_order_d -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg
>
> but, i got fatal error:-
>
> Taking z axis as normal to the membrane
> Reading file md_0_1.tpr, VERSION 3.3.2 (double precision)
> Using following groups:
> Groupname: System First atomname: C1 First atomnr 0
> Groupname: POPC First atomname: C1 First atomnr 0
> Groupname: SOL First atomname: OW First atomnr 6656
>
> Reading frame       0 time    0.000   Number of elements in first 
> group: 14036
>
> -------------------------------------------------------
> Program g_order_d, VERSION 3.3.2
> Source code file: gmx_order.c, line: 360
>
> Fatal error:
> grp 1 does not have same number of elements as grp 1
>
> i have deleted the group 0-2, but why is it it still read the group 0 
> which the "system" that consist of 14036 atoms?
>
> i would be grateful of anyone can advice on this.
>
> Thanks in advance.
>
> Regards,
> bing
>
>
>
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>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys