[gmx-users] Dihedral Population Analysis -Index file
ramezanpour.mohsen at gmail.com
Tue Jan 24 21:46:13 CET 2017
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.
On Tue, Jan 24, 2017 at 3:56 AM, Mark Abraham <mark.j.abraham at gmail.com>
> 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,
> > 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
> > system.
> > In my index file, I made it based on the atom numbers in the topology
> > 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
> > 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
> Something along the lines of
> resname POPC and name C2 C3 C4 C5
> will produce a group that has that dihedral from every POPC.
> > Thanks in advance for any comment and suggestion
> > Cheers
> > Mohsen
> > --
> > *Rewards work better than punishment ...*
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