[gmx-users] gromacs.org_gmx-users Digest, Vol 119, Issue 23

Eric Smoll ericsmoll at gmail.com
Thu Mar 6 00:48:22 CET 2014

> Message: 2
> Date: Wed, 5 Mar 2014 07:04:53 +0200
> From: Teemu Murtola <teemu.murtola at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] gmx gangle in the development version of
>         gromacs
> Message-ID:
>         <CAB5URpa=Kyczq-OJQxxZRa5QXmn4QSq0VKc3sg3LQe=
> Hqi8nJw at mail.gmail.com>
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> Hello,
> On Wed, Mar 5, 2014 at 1:30 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
> > Assuming I define a given slice to be between 0 and 1 on the z axis, I
> >
> believe the command that will produce what I want is:
> >
> > gmx gangle -f file.trr -s file.tpr -n  file.ndx -g1 plane -group1 'z 0
> to 1
> > and group a_plane' -g2 z -oh file.xvg -binw 1.0
> >
> > A few questions/comments:
> >
> > 1.) I am unsure how I should set the '-selrpos' option. The gangle
> program
> > requires all three atoms to compute the angle so I suspect that the
> prefix
> > 'whole_' is necessary. What is the difference between the "res_" and
> "mol_"
> > infix?  I was hoping the index file would restrict the computation of the
> > reference position so that 'whole_res_cog' would work but it seems to
> > compute the cog for the whole residue, not that atoms that define the
> > plane.  For clarity, if the cog of the three atoms that define the plane
> > lie within the slice, I want all three atoms that define the plane to be
> > selected.
> >
> As you have noted, whole_res_cog computes the center-of-geometry of the
> whole residue that contains an individual atom. So if each of your rings is
> within a single residue, this makes then selected as a unit, based on the
> center of the whole residue. If you only want to select based on the center
> of the ring, you can use part_res_cog. The difference is explained in 'gmx
> help selections positions' (accessible also when writing "help" in the
> interactive selection prompt).

I will try part_res_cog but I suspect it is not what I want. 'gmx help
selections positions'
"part_ prefix calculates the centers for the selected atoms, but uses
always the same atoms
for the same residue/molecule. The used atoms are determined from the the
largest group allowed by the selection."
This first sentence sounds like it may preform the selection I desire but
the second
sentence is worrisome.  I have a molecule with a ring. My index file
selects three atoms from this molecule to monitor - three atoms are needed
for an normal
vector calculation. If a cog is in the selection region but only one of the
three atoms that
define a given cog are in the selection region, will 'part_res_cog' result
in the selection of all three atoms?

> The difference between res_ and mol_ is that res_ groups the atoms by
> residue index for calculating the center, while mol_ groups by molecule.
> There is a difference if your molecules consist of multiple residues. For
> small molecules like benzene, you probably have a single residue number for
> each molecule, and the options are equivalent.

If the residue index controls which atoms are grouped in a given 'residue',
controls the molecule specification?  What is it in the .gro file that
defines an
atom as belonging to a specific molecule?

> 2.) Is it possible to use a custom set of atoms for computation of the cog
> > that differs from the atoms I want selected if this cog is within the
> > slice?  For example, consider benzene. The program gangle requires three
> > benzene atoms to define a plane but the cog of these atoms is not the cog
> > of the ring.  I suspect this is not possible with the gromacs tools.
> >
> It is possible to use either the center of the three atoms, or the center
> of the residue/molecule, as explained above. Other alternatives are not
> currently supported, except through splitting your molecule into multiple
> residues (it should be possible by simply editing the residue numbers in a
> gro file passed to the -s option to make this happen).

This sounds like a very straightforward solution! I read up on the format
of the
.gro file.  It makes sense that I should be free to manipulate the residue
but are they any restrictions? For example. do the residue numbers need to
be grouped and
consecutive? I ask because a separate software (VMD) will not support
residue number reassignment
of various nonconsecutive atoms without disrupting the residue selection

> > 3.) It seems the flag '-oall' outputs the angles for all the normal
> vectors
> > defined by the atoms in my index file.  Is this want most users will want
> > from this tool?  If I have selection like 'z 0 to 1 and group a_plane',
> it
> > makes more sense for '-oall' to print all the selected angles, correct?
> >
> Maybe, but the current implementation is a compromise that also makes it
> easier to use that information for post-processing. If you want to follow
> the evolution of an individual angle, it will be very difficult if the
> number of angles on the output rows varies, and the angle at a given column
> is not always computed from the same atoms.

I understand and agree.

> You can use 'gmx select -om' with the same selection (possibly prefixed
> with 'res_cog of' to produce a single number per residue) to produce a
> bitmask that you can see which angles are actually getting selected, and
> correlate this with the -oall output.
> This sounds useful.  Thank you for the suggestion!

> Hope this helps,
> Teemu

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