[gmx-users] g_order in a micelle

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 14 16:07:48 CET 2007

Jonathan Khao wrote:
> Hello, 
> I'm trying to get the order parameter of lipids in a micelle, so i've
> decided to make a script that makes a trjconv of individual lipids, with
> a fit to a structure that is aligned along the Z axis.
> Now that I have the trajectories, i'm trying to launch g_order. The
> problem is that it requiers a tpr file that I don't have. I have tried
> to generate one using a modified mdp, top, and gro file , but i get a
> semgentation error. 
> Is it possible to get a Tpr from a Trr ?
> Or even better , is it possible to make a g_order with a defined vector
> instead of the three axis ? 
> Thanks.
you can use tpbconv with an index file to make a tpr for one lipid from 
your original tpr file.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list