[gmx-users] Re: dihedral angles
Luca Mollica
mollica.luca at hsr.it
Wed Feb 25 13:14:01 CET 2004
>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
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