Carla Jamous wrote:
Thank you,
It worked, one last question. Something is not very clear to me:
-ov: plots the average angle of a group of angles as a function of
time!! What does it mean?
Because I'm getting positive and negative values in the same plot. Are
these values the values of my dihedral angle as a function of time?
The -ov option gives the average angle of all angles contained in the index
group over time. If your selected group contains only one angle, then the
average at any given time is equal to the instantaneous value at that time.
-Justin
Thanks again,
Carla
On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey <kgp.a...@gmail.com
<mailto:kgp.a...@gmail.com>> wrote:
try the -type option with dihedral
amit
On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous <carlajam...@gmail.com
<mailto:carlajam...@gmail.com>> wrote:
Hi Everyone,
Please I'm trying to calculate one dihedral angle as a function
of time during my simulation.
For this, I used g_angle. In the manual (version 4.0.3) it says:
the indexfile should contain atom-triplets or atom-quadruplets
for dihedrals.
I put an atom-quadruplet in my index file, but when I run
g_angle -f .xtc -n .ndx -od .xvg
and I select the group of atom-quadruplets, gromacs crashes and
shows this error message:
number of index elements not multiple of 3, these can not be
angle triplets
So actually g_angle only calculates angles not dihedrals?
Thanks
Carla
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
