[gmx-users] Order parameters of lipid

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 31 12:05:21 CEST 2008

minnale wrote:
> I want to calculate order parameters of palmitoyl and oleyl chains of 
> POPC which ran it for 5ns, so I have done below mentioned steps.
> 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx 
> command and selected a C34|a 035|a C36.....a C50.
> In index file the palmitoyl chain selected like this C34_O35_C36......C50

You need the index groups to specify each atom separately, and only include 
carbon atoms.  Your index group will be something like:

[ C34 ]
[ C36 ]
[ C50 ]

> 2. This index file feed to g_order command
>     g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od scd.xvg -unsat

There are no unsaturated carbons in a palmitoyl chain.


>   This programming is running very slowly
> Have I done any mistake here?
> I would be thankful for your help
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list