[gmx-users] Dihedral Population Analysis -Index file

[Mohsen Ramezanpour]

Thanks Mark. That is great.

I tried that and I made an Index file of what I want.

"DIH" resname DOPC and atomname O  C12  C23  C


However, looking at index files, the order of atom numbers is not right and
give me a wrong dihedral for analysis with g_angle.

8101  8116  8117 8126


*I want it to be like:*
*8117  8116   8126   8101*  (based on atom numbers in the .gro file)
because the order matters for the dihedrals.

So, I used the following one but it did not work neither:
"DIH" resname DOPC and atomname O  C12  C23  C  permute 1  2  3  4
To keep them in the order they are (I assumed 1, 2, 3, 4 represents the
position of atom names in command), and the out put is again:

8101 8116 8117 8126 which is wrong again.

If I assume that the numbers are the positions for atom numbers (not the
atomnames), then 1 would be for 8101, 2 for 8116, 3 for 8117, and 4 for 8126
"DIH" resname DOPC and atomname O  C12  C23  C  permute  3  2  4  1

and the output will be:
8126 8116 8101 8117

Which is not what I want.
Could you please clarify how to make the order as I want?
I read but could not figure it out.

Thanks.


On Tue, Jan 24, 2017 at 3:56 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Tue, Jan 24, 2017 at 12:35 AM Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I have a trajectory file which I wish to do a dihedral analysis for
> > specific dihedral.
> > Based on what I understood from mailing list and manual, I made an
> > index.ndx manually for the dihedral of interest in the molecule.
> >
> > Usually, when we make an index file, say for atom P in the system,
> make_ndx
> > makes an index file which includes the numbers for all the P atom in the
> > system. These numbers are the index numbers in the .gro file for the
> whole
> > system.
> >
> > In my index file, I made it based on the atom numbers in the topology
> file
> > for the lipid.
> >
>
> That forces you to use a trajectory file that contains only a single lipid.
> With suitable index groups (for which I recommend gmx select), there's no
> need to do that.
>
>
> > For doing analysis, I first used trjconv and saved only the .xtc file for
> > only the lipid of interest, and then used g_angle to calculate the
> dihedral
> > population. I think what I get is only for ONE lipid over time NOT an
> > average over time and lipids in the system.
> >
>
> Perforce. You only gave gmx angle one lipid and used an index group with
> one dihedral. Whether you got a time series, an average or a distribution
> depends on what you did with gmx angle.
>
>
> > The obvious solution would be to include all the dihedrals for all the
> > lipids in it.
> > BUT, this is not easy to do manually. I tried mk_angndx but it is not
> > giving me what I want.
> > Is there any way to do this?
> >
>
> Sure, see
> http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
>
> Something along the lines of
>
> resname POPC and name C2 C3 C4 C5
>
> will produce a group that has that dihedral from every POPC.
>
> Mark
>
>
> > Thanks in advance for any comment and suggestion
> >
> > Cheers
> > Mohsen
> >
> > --
> > *Rewards work better than punishment ...*
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-- 
*Rewards work better than punishment ...*