[gmx-users] g_select question

Teemu Murtola teemu.murtola at gmail.com
Wed May 8 17:55:53 CEST 2013


On Wed, May 8, 2013 at 4:44 PM, Albert <mailmd2011 at gmail.com> wrote:

> I am trying to run g_select with command:
> g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat
> in the selection.dat I defined the following:
> watero= name 0 and resname T3P;
> close = water0 and within 0.6 of resid 50;
> close;
> my residue 50 is in the deep pocket of protein and there is only max. 12
> water near 6A. However, I found that in almost all my trajectories, there
> are at least 16 water from the g_select output. I am just wondering, is
> there anything wrong of my defenition in selection.dat?

There's nothing obvious wrong with the selections (if you don't count
mismatches between the letter O and the number 0, which should give you
errors if you really had those in your input). You can try to diagnose the
issue with the -oi and/or -on flags for g_select to see what exactly gets
selected. You should also ensure that "resid 50" selects the residue you
expect and nothing else.

If you think that something is getting selected incorrectly, please provide
additional information like your Gromacs versions and what exactly is
selected and why it shouldn't.


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