[gmx-users] gmx gangle in the development version of gromacs
teemu.murtola at gmail.com
Thu Mar 6 05:57:45 CET 2014
On Thu, Mar 6, 2014 at 1:48 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
> > 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
> > 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
> > of the ring, you can use part_res_cog. The difference is explained in
> > 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?
Yes, it will. If you have a selection like
name A B C and z > 0
and your residue has atoms A B C D E, then
- -selrtype whole_res_cog will select either all or none of A-C, based
on the CoG of A-E.
- -selrtype part_res_cog will select either all or none of A-C, based on
the CoG of A-C.
- -selrtype dyn_res_cog will in this case do the same as part_res_cog.
It requires quite a complex selection to make a difference between the two
(for example, "name A B C and atom z > 0 and dyn_res_cog x > 0", in which
case the second "x > 0" condition only compares based on the CoG of the
atoms that satisfy "z > 0"). This is probably confusing and not usually
necessary; it mostly makes sense as an output option from the selections
only: "dyn_res_cog of name A B C and z > 0" computes the output position
from those atoms that actually satisfy the z > 0 condition.
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?
There is nothing in a .gro file that specifies a molecule. This option only
works with a full .tpr file, in which case the molecule definitions from
the simulation topology are used.
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
In Gromacs, a group of consecutive atoms with the same residue number is
treated as a single residue. If the same residue number repeats elsewhere,
then it is a different residue. There is no requirement on the numbers of
different residues being consecutive. So the atoms in a residue need to be
grouped together, but there are no other restrictions. Depending on what
you want to do with the numbers, it can be confusing, though, if the same
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