[gmx-users] Dihedral Population Analysis -Index file

[Mark Abraham]

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
>
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