[gmx-users] Cannot combine residue position based cog selection with index output for g_select

Mark Abraham mark.j.abraham at gmail.com
Sun Oct 26 12:21:58 CET 2014


I'm not the expert here, but I think that gmx select -selrpos has options
that you should be able to use here. See gmx help selections positions


On Fri, Oct 24, 2014 at 10:43 PM, Huang Dongxu <fredhdx at gmail.com> wrote:

> Hi,
> I have a system consists of a box of water and a monolayer of polymer in
> the center. I am trying to extract solvent molecules that have z
> coordinates greater than 5 nm using g_select and output an index file.
> Basically I want to separate my system into two portions: a box of waters
> above the monolayer and the rest of the system containing the monolayer.
> With the water only portion extracted by trajconv, I want to use genion to
> replace some water molecules with salt and put this modified portion back
> to my system that contains the monolayer.
> Right now, I am able to use g_select -on -select "resname SOL and z>5" to
> select all atoms that belong to SOL and has z > 5 nm. However, this way
> does not guarantee that all the atoms selected are from SOL molecules whose
> cog are above z=5 plane. And as a result, some atoms that are part of SOL
> molecules below the z=5 plane are also selected and the entire selection
> contains some complete water molecules and some atoms that are from below
> plane water molecules (incomplete waters).
> I am not sure with this kind of selection, if I extract it with trajconv,
> and replace water with salt by genion, and then put it back to original
> system, will I get correct alignment of those atoms from incomplete water
> molecules and get the desired configuration. ( I think genion will only
> replace complete residue; however, when using trajconv to generate new
> coordination files, I am not sure if the system will be re-set to origin or
> not. If so then the coordinates will definitely be misplaced and when I put
> the modified part back there will be misalignment).
> TO AVOID all that, I'd like to use "cog of SELECTION" option in the
> g_select, except for 1 problems: the -on option only works with atom
> selection.
> So my essential question is: is there a way to use g_select with both the
> -on option and cog option? Or is there another way to finish my task?
> I have searched the archive and did not find something that answers my
> question.
> Thank you all for helping out.
> Best,
> Dongxu Huang
> Graduate student at Northwestern University
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