[gmx-users] How to select the molecules within a defined radius

Teemu Murtola teemu.murtola at cbr.su.se
Mon Feb 15 21:00:56 CET 2010


On Mon, Feb 15, 2010 at 19:04, Saikat Banerjee <banskt.saikat at gmail.com> wrote:
> I selected a sphere at a fixed center and noted the
> number of water and DMSO molecules within that cut-off. I would like to know
> if there are any methods to do the same within GROMACS.

The development (git) version of Gromacs has for some time included a
tool called g_select, which should be able to do what you want.
There's only limited documentation, but 'g_select -select help' and
'g_select -select "help cmdline"' should give something to start with.
Your problem could be solved with something like

g_select -select 'resname DMSO and within 1.0 of (2.0, 2.0, 2.0)'
-seltype res_com -selrpos res_com -os

which gives you the number of DMSO centers of mass within 1 nm of the
given point as a function of time.

If you feel like testing it, any feedback is welcome.

- Teemu

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