[gmx-users] How to calculate the angle between the bilayer normal and the P−N vector?

[Ezequiel Frigini]

Dear gromacs users,

I need to calculate the angle between the bilayer normal and the P−N vector.

Gathering information (but I'm not sure), I think one way to do this is:

1- Generate an index.ndx with g_selection of all the P and N of a monolayer.

2- Then use g_bundle as follows:

   g_bundle -f xxx.xtc -s xxx.tpr -n index_P_N.ndx -z -na 1 -o angulo_PN.xvg

I'm not sure if this is okay. Primarily if "-z" is the normal of the
bilayer. Also, I'm not clear why "-na" should be 1.

Thank you in advance!


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Ezequiel Nazareno Frigini
Lic. en Biología Molecular
Grupo de Bioinformática Estructural
bios.unsl.edu.ar

Instituto de Matemática Aplicada San Luis, IMASL.
Universidad Nacional de San Luis - CONICET.
Calle Ejercito de Los Andes 950
D5700HHW San Luis. Argentina.

Tel: +54 266 4520300 int. 3046

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