[gmx-users] Dihedral Population Analysis -Index file

[Mohsen Ramezanpour]

Thanks Mark. It works now.
I did the same for other dihedrals and everything looks fine.

Cheers
Mohsen


On Wed, Jan 25, 2017 at 3:10 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Permutations are tricky to describe, but the code looks like it works the
> way
> http://manual.gromacs.org/documentation/5.1/onlinehelp/
> selections.html#permuting-selections-permute
> describes. You want 4 2 1 3
>
> Mark
>
> On Tue, 24 Jan 2017 21:46 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com
> >
> wrote:
>
> > 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 ...*