Dear all, Recently, I have performed simulation on a B-DNA using gromacs, and I want to use g_order in gromacs to get the order parameters for the bonds C1'-H1', C3'-H3'. Is it possible to obtain order parameters for these two bonds with g_order? If possible, Would you please tell me the correct way to get order parameters for C1'-H1', C3'-H3'?
Thank you very much! jnsong P.S. I just had a try using g_order, the process is as follows: ------------------------------------------------------------------------- > a C1' Found 24 atoms with name C1' 11 C1' : 24 atoms > a H1' Found 24 atoms with name H1' 12 H1' : 24 atoms > del 0-10 Removed group 0 'System' Removed group 1 'DNA' Removed group 2 'K' Removed group 3 'CL' Removed group 4 'Water' Removed group 5 'SOL' Removed group 6 'non-Water' Removed group 7 'Ion' Removed group 8 'K' Removed group 9 'CL' Removed group 10 'Water_and_ions' > q --------------------------------------------------------------------------------- through this I get index.ndx for C1'-H1' and then I perform: > g_order -f md.xtc -s md.tpr -n index.ndx -o and I get order.xvg, but there are no order parameters in order.xvg and the contents of order.xvg are as follows: ---------------------------------------------------------------------------------- # This file was created Thu Nov 10 20:00:06 2011 # by the following command: # g_order -f md.xtc -n index.ndx -s md.tpr -o -ob # # g_order is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @ title "Order tensor diagonal elements" @ xaxis label "Atom" @ yaxis label "S" @TYPE xy ---------------------------------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
