[gmx-users] How to analyze order parameter

Kukol, Andreas a.kukol at herts.ac.uk
Thu Jul 3 12:05:41 CEST 2008

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

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of anirban polley
Sent: 03 July 2008 10:10
To: gmx-users at gromacs.org
Subject: [gmx-users] How to analyze order parameter

         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.

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