First, make an index file that contains one group each for every carbon atom in the acyl-chain (starting with the carbonyl-carbon and going further down).
You need to make two index files: for sn1 and sn2 chains of DPPC Then you get the deuterium order parameters for each atom with the output option -od to g_order Best wishes Andreas >>>> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of anirban polley Sent: 03 July 2008 10:10 To: gmx-users@gromacs.org Subject: [gmx-users] How to analyze order parameter Hi, I want to find deuterium order parameter of the system of DPPC+SM+CHOL+WATER g_order -f traj.trr -s topol.tpr -n index.ndx -dt 0.001 it gives the following error: Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 3.3.3 (single precision) Using following groups: Groupname: System First atomname: C1 First atomnr 0 Groupname: DPP First atomname: C1 First atomnr 0 Groupname: SM First atomname: C1 First atomnr 1000 Groupname: CHOL First atomname: C1 First atomnr 2000 Groupname: SOL First atomname: OW First atomnr 2580 trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Number of elements in first group: 3180 ------------------------------------------------------- Program g_order, VERSION 3.3.3 Source code file: gmx_order.c, line: 360 Fatal error: grp 1 does not have same number of elements as grp 1 ------------------------------------------------------- How can I analyze the order parameter my system? Can you answer my question? I don't understand what to do. Regards, Anirban _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
