[gmx-users] Calculate dihedrals

[Alessandra Villa]

Hi,

On Wed, Mar 25, 2020 at 1:10 PM Marko Petrovic <marko at kth.se> wrote:

> Hello
>
> I want to calculate som singular dihedral values and I know this is
> simple, but can't figure out the usage of "gmx gangle" . I tried using "gmx
> angle" but the results were not what I was hoping for as it calculates an
> average of the specified angles and seems to be meant for averaging many
> angles calculations.
>
You can use gmx angle with the  -all option. With the option -all the first
graph is the average and the rest are the individual angles. Or in
alternative use an index file with 1 dihedral angle
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-angle.html?highlight=gmx%20angle


> Using the .gro and .ndx files from my call to "gmx angle"
>
> gmx angle -f start.gro -n test.ndx -type dihedral
>
> to a all to "gmx gangle"
>
> gmx gangle -g1 dihedral -f start.gro -n test.ndx
>
> You could try to add the option  -group1 selection
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-gangle.html?highlight=gmx%20gangle

Best regards
Alessandra


> this starts a dialogue where I initially tried selecting groups defined in
> the .ndx file, no error message suggests I've been successful. Pressing
> ctrl+d ends the run with the following message:
>
>     > Reading frames from gro file 'GROningen Mixture of Alchemy and
> Childrens' Stories', 22 atoms.
> Last frame          0 time    0.000
> Analyzed 1 frames, last time 0.000
>
> But I can't find any output  anywhere. What am I missing?
>
>
> With Regards
> Marko Petrovic
> Educator
> Computational Science and Technology
> School of Electrical Engineering and Computer Science
> KTH Royal Institute of Technology
> --
> Gromacs Users mailing list
>
> * 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-request at gromacs.org.