Dear all,<br>I had created 3-21 group of sn1 chain for order analysis. I have issued:-<br><br>make_ndx_d -f md_0_1.tpr -o sn1.dx<br><br>> a C15<br><br>Found 128 atoms with name C15<br><br> 3 C15 : 128 atoms<br>
<br>> a C16<br><br>Found 0 atoms with name C16<br>Group is empty<br><br>> a C17<br><br>Found 128 atoms with name C17<br><br> 4 C17 : 128 atoms<br><br>> a C18<br><br>Found 128 atoms with name C18<br>
<br> 5 C18 : 128 atoms<br><br>> a C19<br><br>Found 128 atoms with name C19<br><br> 6 C19 : 128 atoms<br><br>> a C20<br><br>Found 128 atoms with name C20<br><br> 7 C20 : 128 atoms<br>
<br>> a C21<br><br>Found 128 atoms with name C21<br><br> 8 C21 : 128 atoms<br><br>> a C22<br><br>Found 128 atoms with name C22<br><br> 9 C22 : 128 atoms<br><br>> a C23<br><br>
Found 128 atoms with name C23<br><br> 10 C23 : 128 atoms<br><br>> a C24<br><br>Found 128 atoms with name C24<br><br> 11 C24 : 128 atoms<br><br>> a C25<br><br>Found 128 atoms with name C25<br>
<br> 12 C25 : 128 atoms<br><br>> a C26<br><br>Found 128 atoms with name C26<br><br> 13 C26 : 128 atoms<br><br>> a C27<br><br>Found 128 atoms with name C27<br><br> 14 C27 : 128 atoms<br>
<br>> a C28<br><br>Found 128 atoms with name C28<br><br> 15 C28 : 128 atoms<br><br>> a C29<br><br>Found 128 atoms with name C29<br><br> 16 C29 : 128 atoms<br><br>> a C30<br><br>
Found 128 atoms with name C30<br><br> 17 C30 : 128 atoms<br><br>> a C30<br><br>Found 128 atoms with name C30<br><br> 18 C30 : 128 atoms<br><br>> a C31<br><br>Found 128 atoms with name C31<br>
<br> 19 C31 : 128 atoms<br><br>> a CA1<br><br>Found 128 atoms with name CA1<br><br> 20 CA1 : 128 atoms<br><br>> a CA2<br><br>Found 128 atoms with name CA2<br><br> 21 CA2 : 128 atoms<br>
<br>>del 0-2<br><br>Removed group 0 'System'<br>Removed group 1 'POPC'<br>Removed group 2 'SOL'<br><br>Subsequently, i did this:-<br><br>g_order_d -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg<br>
<br>but, i got fatal error:-<br><br>Taking z axis as normal to the membrane<br>Reading file md_0_1.tpr, VERSION 3.3.2 (double precision)<br>Using following groups:<br>Groupname: System First atomname: C1 First atomnr 0<br>
Groupname: POPC First atomname: C1 First atomnr 0<br>Groupname: SOL First atomname: OW First atomnr 6656<br><br>Reading frame 0 time 0.000 Number of elements in first group: 14036<br><br>-------------------------------------------------------<br>
Program g_order_d, VERSION 3.3.2<br>Source code file: gmx_order.c, line: 360<br><br>Fatal error:<br>grp 1 does not have same number of elements as grp 1<br><br>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?<br>
<br>i would be grateful of anyone can advice on this.<br><br>Thanks in advance.<br><br>Regards,<br>bing<br><br><br><br>