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 <jalem...@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 <jalem...@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
jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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mail to gmx-users-requ...@gromacs.org.
