[gmx-users] problem in g_order

[Bing Bing]

Dear Erik,
oo.....i will be more meticulous next time.
It works. :)
thanks again.

Regards,
bing

On Thu, Jul 2, 2009 at 9:38 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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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>
>
> --
> -----------------------------------------------
> 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
>
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