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 > 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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