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

[lazaro monteserin]

Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files:

I followed the protocol in gromacs website to do dihedral Principal
Component Analysis:

1) Created an index file (*dangle.ndx*) with a list of the dihedrals to
analyze from my molecule. I wrote this file in a text editor by hand as we
discussed before.

2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD
in the file (*dangle.trr*) with the following command:
*gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral*

(I had 21 angles so it used 14 sin/cos to represent the angles)

3) Then I generated an index file (*covar.ndx*) with a list of numbers from
1 to 14 for trjconv.

4) I runned trjconv to generate the dummy (resized.gro) to use for the
covariance analysis:
*gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e
10000*
10000 was the time in ps for the last frame of the simulation.

5) I runned covar:
*gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit
-nomwa -noref -nopbc*

6) Then I got the PMF along one eigenvector and 2D free energy landscape
for projections along two eigenvectors:
*gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2
-2d 2dproj_1_2.xvg*

7) Then I got the projection in 3D of the free energy landscape:
*gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm
-ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm*

Note: I attached all the files in the dropbox link below
https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0

I would appreciate any feedback

Thank you in advance Dr. Lemkul

Kindly,
Lazaro



On Sat, May 2, 2020 at 8:47 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/30/20 2:07 PM, lazaro monteserin wrote:
> > 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?
>
> The error is coming from xpm2ps which means there's something wrong with
> the .xpm file itself but without seeing how you generated it (exact
> command and description of how you prepared the input data file) and
> perhaps the .xpm file itself (uploaded somewhere), it's impossible to
> comment further.
>
> -Justin
>
> > 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
> >>
> >> * Please search the archive at
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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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