Fw: [gmx-users] p_N head group lipid orientation

[yousef nademi]

----- Forwarded Message -----
From: yousef nademi <yousef_nademi at yahoo.com>
To: Justin Lemkul <jalemkul at vt.edu>
Cc: 
Sent: Friday, July 27, 2012 10:02 AM
Subject: Re: [gmx-users] p_N head group lipid orientation

thank you for responding 
but i want the figure probability versus P-N vector angle and g_sgangle dont give this output .just g_angle give this output


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: yousef nademi <yousef_nademi at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, July 27, 2012 9:57 AM
Subject: Re: [gmx-users] p_N head group lipid orientation



On 7/27/12 12:50 PM, yousef nademi wrote:
> 
> ​hi everybody
> i want to calculate the P_N orientation of dppc lipid bilayer but in g_angle index file shoud have at least 3 atom but in P_N vector i want to define 2 atom
> is there anyone know what should i do?
> 

g_sgangle with the -z option (assuming the bilayer is in the x-y plane) should do this.  The index group can contain two atoms (or a suitable multiple of two defining all the P and N atoms).

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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