On 5/2/20 3:12 PM, lazaro monteserin wrote:
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
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
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
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
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
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? Kindly,
Lazaro
On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote:
>
>
> On 4/29/20
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
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?
Any help would be very appreciate it.
Kindly,
Lazaro
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