[gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

Yes ,I am using cg model.

On Dec 13, 2019 2:37 PM, "Alessandra Villa" <
alessandra.villa.biosim at gmail.com> wrote:

Hi,

On Thu, Dec 12, 2019 at 1:09 PM SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> hi,
> i want to calculate the tilt angle of helix against the bilayer normal.
> First i made a index file which contains the backbone of the residues of
> large helix. I am using this command
> *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
> -oradius -otwist -obending -otilt -orot*
> my questions are
>
> 1. Should i mention any other residues in index file so that the angle can
> be calculated along the bilayer normal.
>

As far as I know, four Calpha coordinates are used to define the local
direction of the helix
axis (
http://manual.gromacs.org/current/onlinehelp/gmx-helixorient.html?highlight=
gmx%20helixorient
)
. but I am not sure to what those Calphas correspond since you are using a
CG model.

Best regards
Alessandra

2. by using this command i am able to analyse for 1 us coarse grained
> simulation. But for the next 1 us run i am getting this error
> "too many iterations in routine jacobi"
> can anyone please guide me.
> thanking you
> shahee
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