Re: [gmx-users] g_order in a micelle
Problem solved, thanks ! > 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. > -- Jonathan KHAO LISM-IBSM-CNRS 31 Chemin Joseph Aiguier 13402 Marseille Cedex 20 France [EMAIL PROTECTED] tel : 0616738391 ___ gmx-users mailing listgmx-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
Re: [gmx-users] g_order in a micelle
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. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
[gmx-users] g_order in a micelle
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. -- Jonathan KHAO LISM-IBSM-CNRS 31 Chemin Joseph Aiguier 13402 Marseille Cedex 20 France [EMAIL PROTECTED] tel : 0616738391 ___ gmx-users mailing listgmx-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
