[gmx-users] Re: dihedral angles

[Luca Mollica]

 >Hi
 >I have simulation of phospholipid menbrane and I need to calculate >trans
 >fraction as a function of position of dihedral angle in lipid chain (I 
 >means
 >that the points on x axis will be - (dihedral between C1A,C1B,C1C, C1D 
 >as a
 >1st point; dihedral between C1B,C1C,C1D, C1E as a 2nd point; etc.).
 >I alse need to calculate the transition time as a function which 
depend >on
 >same thing as the function above. But I don't know, how to compute it >(I
 >suppose I sould use a g_angle).

Hi Milan,

the kind of analysis you describe can be performed in the following way:

1. First define the planes that form the dihedral angle you are 
interested in, e.g., if you consider atoms C1A,C1B,C1C, C1D, then you 
have to define planes C1A-C1B-C1C and C1B-C1C-C1D. You have to define 
them using make_ndx and selecting atoms by numbers.

2. Then, you have to use g_sgangle, that considers normals to planes and 
computes angles between them (it outputs cos of the angle). The putput 
has to be flagged with -oa:

........................................

-oa: Angle between the two groups specified in the index file. If a group
contains three atoms the normal to the plane defined by those three 
atoms will
be used. If a group contains two atoms, the vector defined by those two 
atoms
will be used.

........................................

In this way, you can check for dihedral angles changes during the 
simulation.

Bye

L



 >Thanks for an advice.

 >Milan

 >ps: if it is not clear what I meaned by X axis, I can send a picture 
 >with
 >similar graph I need.





*******************************************************************************************************

Luca Mollica
Dulbecco Telethon Institute (Biomolecular NMR Unit)

DIBIT-HSR,Via Olgettina 58, 1B4
20132 Milano (Italy)

Tel: 0039-02-26434824
Fax: 0039-02-26434153
E-mail: mollica.luca at hsr.it