[gmx-users] P-N vector orientation

[patrick fuchs]

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
>>
>>
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-- 
_______________________________________________________________________
!!!! new E-mail address: patrick.fuchs at 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