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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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