[gmx-users] g_select question

Albert mailmd2011 at gmail.com
Wed May 8 15:44:58 CEST 2013


  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;

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?

thank you very much


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