[gmx-users] p_N head group lipid orientation

[Justin Lemkul]

On 7/27/12 1:02 PM, yousef nademi wrote:
> 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
>

g_analyze -distr produces distributions from any .xvg file, otherwise it is 
fairly straightforward to write a simple histogram program.

-Justin

>
> ----- 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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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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