Re: [gmx-users] P-N vector orientation
Hi, as Nicolas suggested you can use my program g_tilt to do such an analysis. Instead of giving the whole backbone as a selection, simply give the 2 atoms (P N). Initially g_tilt uses the first eigen vector of the inertia matrix of the atom selection, so you might want to simplify the code to calculate the PN vector (using [xN-xP,yN-yP,zN-zP]). Ciao, Patrick Nicolas a écrit : Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ http://www.dsimb.inserm.fr/%7Efuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P-N vector orientation
Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ http://www.dsimb.inserm.fr/%7Efuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] P-N vector orientation
Hi, g_bundle does something similar, so does g_sgangle (but only for one vector I think). Berk Date: Thu, 12 Feb 2009 10:50:02 -0700 From: nsa...@ucalgary.ca To: aninditaga...@yahoo.co.in; gmx-users@gromacs.org Subject: Re: [gmx-users] P-N vector orientation CC: Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ http://www.dsimb.inserm.fr/%7Efuchs/download/ Its purpose is to calculate the orientation of an helix in a bilayer, however it might tweaked to calculate the NP dipole orientation. I've done that one time, but it was only for a particular lipid in a membrane, not for the whole bilayer. IIRW, the result was the same than the one of my scripts and the calculation was much faster. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P-N vector orientation
Hello, Is that thread solved? I've got a bunch of TCL scripts for VMD that can do this calculation. They are not really user friendly or incredibly fast, but they give a correct answer. I can send those scripts off the list if you are interested. Nicolas ANINDITA GAYEN a écrit : Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php begin:vcard fn:Nicolas Sapay n:Sapay;Nicolas org:University of Calgary;Biological department adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada email;internet:nsa...@ucalgary.ca title:Post-doctoral fellow tel;work:403-220-6869 x-mozilla-html:TRUE url:http://moose.bio.ucalgary.ca/ version:2.1 end:vcard ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] P-N vector orientation
Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P-N vector orientation
Hi Anindita, This program I had a long time ago and unfortunately it has been lost during my movings. I think you should try to contact: Andrei. Gurtovenko Biophysics and Soft Matter Group Laboratory of Physics Helsinki University of Technology P.O.Box 1100 FIN-02015 HUT Finland Tel.: +358-9-4515803 e-mail: a...@fyslab.hut.fi He had a version and if my memory is correct he modified it to an even better version. It would actually be useful if someone could post a existing version of PN orientation. XAvier. On Feb 10, 2009, at 2:12 PM, ANINDITA GAYEN wrote: Dear Xavier Periole I am a GROMACS user, presently working with DMPC bilayer.. I want to calculate the orientation of the head groups P-N vector. From gmx-users, I have came to know that you have a program that can determine the angle of the PN vector (or what ever pair of atoms) relative to the z axis. If possible, can you please provide me that program or tell me how can i calculate that? Thanks in advance. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now.___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
