[gmx-users] about how to create angle.index with specific angles

[lazaro monteserin]

Dear Dr. Lemkul I did it. It works. Thank you very much for the advise.

Now I am having issues opening the (.xpm) files generated that contain for
example the gibbs energy landscape on the two first eigenvectors of the
dPCA.

If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps"
it write this error: "Input error or input inconsistency:
Invalid XPixMap"

Do you know if I am missing something here? Do I have to install something
in my OS to be able to see .xpm images?

Thanks in advance,

Lazaro

On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/29/20 7:11 PM, lazaro monteserin wrote:
> > Dear Dr. Lemkul it could be possible use that angle.index with the
> selected
> > dihedrals written by hand as index file for gmx angle for dihedral
> > Principal Component Analysis?
>
> You can create index groups however you like for whatever analysis you
> want to perform.
>
> -Justin
>
> >   Kindly,
> > Lazaro
> >
> > On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 4/29/20 5:01 PM, lazaro monteserin wrote:
> >>> Dear gromacs users,
> >>>
> >>> Is there any way to tell gmx mk_angndx to create the index file with
> >>> dihedral angles from a (.tpr) for specific atom numbers (atom level,
> e.g
> >> 1,
> >>> 2, 3) from my molecule?
> >> mk_angndx is designed for distributions of similar angles (e.g.
> >> evaluating force field sampling). If you want to compute specific
> >> angles, use make_ndx or simply write the index groups by hand.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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